I would say, they do carry over.
The supernatural ability Alternate Form reads (in part):
The creature gains the physical ability scores (Str, Dex, Con) of its
new form. It retains the mental ability scores (Int, Wis, Cha) of its
original form. Apply any changed physical ability score modifiers in
all appropriate areas with one exception: the creature retains the hit
points of its original form despite any change to its Constitution.
It doesn't say here, whether physical ability damage from poison or disease taken prior to the change has to be applied to the new ability scores.
But for several reasons, I think, that should be done.
- Alternate Form does not heal a creature in any way. It does not end effects from poison or disease and it isn't said anywhere, that it would remove ability damage. So, a creature is still afflicted by poison/disease when in alternate form and should consquently still suffer from the ability damage effect.
- The rules on poison, disease and ability loss don't give any indication that ability damage could be overcome by anything else than healing, rest or appropriate spells, like restoration et al.
- Also, according to the Main FAQ (which should be treated with caution, I know), ability damage taken while in wild shape is carried over to the normal form. So, to me, it seems natural that this should also be true vice versa. - Wild shape functions in most respects like alternate form.
If a wild shaped character takes Constitution damage or drain, which
Con score do I use to determine when the character is killed by being
reduced to 0 Con—the original score or the new one?
character’s current Constitution score, just as you would for any
other character. If a 6-Con druid wild shapes into a 17-Con dire
badger and takes 8 points of Constitution damage and/or drain while in
that form, the character would instantly die upon returning to normal
Of course, raising a creature's constitution score results in a better fortitude saving throw modifier – which might help avoid a poison's secondary damage or fight off the disease.