I'm going to paraphrase the questions; I hope that's okay.
When a creature in its original form (form #0) uses a spell of the subschool polymorph to assume different form (form #1) then uses a supernatural ability to assume another different form (form #2), is form #1 now the creature's original form for the purposes of form #2?
This DM is of the opinion that the short answer to that question is No. This DM is also of the opinion that the much longer and more complicated answer is No, but the effects of form #1 can be suppressed by form #2 until the effect causing form #2 is itself ended or suppressed at which time form #1 reasserts itself… and so on. (Note that this DM and player totally understands both the question and the desire!)
Let me first say it's totally possible to get hung up on the question What's a creature's original form? because the game never provides an absolute technical answer to that question and because the game uses what this reader believes are synonyms for the term original form apparently randomly. A contemporary reader attempting a legalistic analysis of the various texts is confronted with a host of seemingly different terms in different contexts. However, to this reader, the same thing is meant by all these terms (see below).
Examples of natural form, normal form, and original form
The term natural form is used by the supernatural ability wild shape (Player's Handbook (2012) 37), the 4th-level Sor/Wiz spell polymorph [trans] (Player's Handbook 263), and the descriptions of, for example, the quasit (Monster Manual 46), succubus (47), imp (56), doppelganger (67–8) and lycanthrope (170).
The term normal form is used by the 2nd-level Sor/Wiz spell alter self [trans] (PH 197), in the description of the chaos beast's supernatural ability corporeal form (Monster Manual 33), and in the lycanthrope entry's description on Changing Form pre-errata (Monster Manual (2003) 178). (Errata changes the section's effects thereby omitting the term rather than changing the term deliberately.)
Both of the terms natural form and original form term are used by the supernatural ability alternate form (Monster Manual 305), but the D&D Glossary on alternate form uses only the term original form in its entry.
This reader can imagine an argument saying that because there's no rhyme or reason to the use of these terms then each term must be a different term that has a different definition that must be gleaned from the term's use exclusively in its own context. Thus each time such a term's used a new definition must be created. That's reasonable, I guess, but that's pretty freakin' intense, and this reader wouldn't do that. Nonetheless, if that's useful in pursuit of a goal, this reader says Go for it.
This reader is far more comfortable with the term original form plus all of its many possible synonyms meaning The creature when any effect that changes its form is absent or suppressed. That is a creature's original form—its form #0. Using this definition means that typically when a creature starting in form #0 changes to form #1 then changes again to form #2, form #1 is ended or suppressed in favor of form #2.
That suppressed part in that definition above is really important. The Player's Handbook on Combining Magical Effects, in part, says
Several other general rules apply when spells or magical effects operate in the same place:…
One Effect Makes Another Irrelevant: Sometimes, one spell can render a later spell irrelevant. For example, if a wizard is using a shapechange spell to take the shape of an eagle, a polymorph spell could change her into a goldfish. The shapechange spell is not negated, however, and since the polymorph spell has no effect on the recipient’s special abilities, the wizard could use the shapechange effect to take any form the spell allows whenever she desires. If a creature using a shapechange effect becomes petrified by a flesh to stone spell, however, it turns into a mindless, inert statue, and the shapechange effect cannot help it escape. (171–2)
(Note that it doesn't matter if, for example, a creature uses a spell to change form then uses a supernatural ability to change form; both are magical effects so this covers both plus spell-like abilities and, by extension (and probably transparency), psionics as well.)
So in that example the wizard (form #0) used the shapechange effect to assume eagle form (form #1) but is then forced by the baleful polymorph effect to assume goldfish form (fort #2). Form #1 has been made irrelevant by form #2 because the wizard is a goldfish not an eagle. The wizard's shapechange spell hasn't ended—it hasn't been dispelled, its duration continues—, but its effect—form #1—has been temporarily suppressed by the baleful polymorph effect that changed the wizard into form #2. The wizard on her turn can take a free action to use the ongoing shapechange effect to assume a form other than form #0 or form #2, and that transformation into a different form functionally swaps form #2 (goldfish) and form #1 (let's say iron golem but it could've as easily been again an eagle). The shapechange effect (form #2) now renders irrelevant the baleful polymorph effect (form #1)… temporarily.
Upon the duration expiring of her shapechange effect (form #2), the wizard normally would automatically assume her original form (form #0) but she's prevented from doing so by the permanent duration of the baleful polymorph effect (form #1). She must do something to end that baleful polymorph effect (form #1) while she's using the shapechange effect to assume a different form (form #2) or else when the shapechange effect ends she'll end up again as a darn goldfish!
And, yes, that is also complicated, too, but it's playable. Changing form in general is already one of the most complicated things in the game, requiring math, patience, research, and a whole lot of time, and one of the most unbalanced effects in a game not well known for being balanced in the first place. My own experience with definitions other than one given above (like, for example, original form meaning a creature's previous form) is that they'll soon have a DM pulling out his hair. This DM advises instituting a definition of original form as meaning The creature when any effect that changes its form is absent or suppressed lest confusion and frustration reign.
Addendum: After writing this, I reread Skip Williams's Rules of the Game columns "Polymorphing Revisited." Part 4 includes the following:
Effects that work some sort of physical change on the recipient fall under the rules for effects that render each other irrelevant. For example, spells such as fins to feet and girallon's blessing from the Spell Compendium both transform the recipient physically…. Since a creature gains the assumed form's body layout and limbs upon changing, the change in form makes either spell irrelevant. For example, if a creature using either spell assumes the form of a horse through alternate form, it becomes a typical horse, with four legs and four feet with hooves. If the creature later reverts to its original form, either spell still applies to the creature, provided the spell's duration hasn't run out.
Despite this reader (and others) sometimes disagreeing with Williams's columns, in this case his opinion and the reader's line up.
Does a creature that's used the spell shapechange to assume a different form keep supernatural abilities derived from classes and levels?
A creature that uses a shapechange effect to assume a different from loses all its original form's supernatural abilities. Despite the creature having kept its classes, levels, and supernatural abilities by way of the spell polymorph then the spell alter self, the spell shapechange says, "You gain all extraordinary and supernatural abilities (both attacks and qualities) of the assumed form, but you lose your own supernatural abilities." The shapechange spell "functions like polymorph, except" for the listed exceptions among which this—the loss of supernatural abilities related to the original form—numbers one. Having druid 17 written on one's character sheet doesn't change the shapechange spell. Simply put, while a a shapechange effect is being used to assume a different form, a creature just can't activate the supernatural ability wild shape.
However, all is not lost! A creature that's the subject of a shapechange effect yet opts not to use that effect to assume a different from its original (or opts to return to its original form) can use its supernatural abilities in that form (form #0). The spell shapechange doesn't itself inherently quash the creature's ability to use its supernatural abilities; it's using the spell shapechange to assume a different form that does. Thus a druid who casts the shapechange spell yet remains in or returns to form #0 can use the supernatural ability wild shape to assume form #1 then use the shapechange effect to assume form #2. Were the shapechange effect subsequently ended or suppressed while the duration of the wild shape continued, the creature would go from form #2 to form #1 instead of from form #2 to form #0.
