Do the secondary effects of protection from evil prevent a Programmed Amnesia spell?

Question

For context I play 3.5e Dnd, and my character has an amulet of Protection from Evil (continuous effect magic item) and an Evil Dragon successfully cast Programmed Amnesia on him despite the second effect of the protection from evil.

Would the second effect of the Protection from Evil (bold text) prevent the effects of a Programmed Amnesia spell (italic text)?

Second, the barrier blocks any attempt to possess the warded creature (by a magic jar attack, for example) or to exercise mental control over the creature (including enchantment (charm) effects and enchantment (compulsion) effects that grant the caster ongoing control over the subject, such as dominate person). The protection does not prevent such effects from targeting the protected creature, but it suppresses the effect for the duration of the protection from evil effect. If the protection from evil effect ends before the effect granting mental control does, the would-be controller would then be able to mentally command the controlled creature. Likewise, the barrier keeps out a possessing life force but does not expel one if it is in place before the spell is cast. This second effect works regardless of alignment.

Programmed Amnesia (Spell Compendium, p.162)

Enchantment (Compulsion) [Mind-Affecting]

Level: Sorcerer 9, Wizard 9,

Components: V, S, M,

Casting Time: 10 minutes

Range: Close (25ft.+ 5ft./2 levels)

Target: One living creature

Duration: Permanent

Saving Throw: Will negates

Spell Resistance: Yes

Answer 1

Probably not, but it depends on your DM's interpretation of the language from Protection from Alignment

I think we can clearly set aside the portions of Protection from Alignment that discuss attempts to possess a target, and enchantment (charm) effects; Programmed Amnesia is clearly neither of those things.

So that means the crux of the question is whether Programmed Amnesia is an:

attempt...to exercise mental control over the creature (including...enchantment (compulsion) effects that grant the caster ongoing control over the subject, such as dominate person)

Programmed Amnesia is unambiguously an enchantment (compulsion) effect, but by my reading, it would not be included in this category, because doing a one-time rewrite of the target's memories is different from the kind of ongoing control over their actions granted by spells like Dominate Person. This is further supported by the subsequent text of Protection from Alignment, which refers to the type of thing it protects against as:

the effect granting mental control

Again, I wouldn't describe something that allows you to rewrite memories as an "effect granting mental control."

However, none of these are reserved rules terms in 3.5e, they're all just being used as their ordinary English meanings. That means there are no rules to check beyond what you've already quoted in your question; how the spells interact is purely up to your DM's interpretation of the language in the spell descriptions.