I encountered yesterday three Shadow Wyrmlings while walking stealthed in the Windy Canyon, and like all dragons, they've inherent True Seeing. However, in EfU the spell should not automatically reveal stealthed opponents and there doesn't even seem to be a bonus to Spot in the modified version. Therefore I find it odd that all three dragons spotted me as soon as I entered their line of sight. My character has a Hide/MS of 19/14 at the moment - not huge, but big enough that this left me wondering, especially since even against a godly Spot/Listen he shouldn't have been instantly revealed as the checks only happen once per round.
I've a vague recollection that merely changing the spell "True Seeing" doesn't necessarily change the permanent TS effect that some monsters have on them as part of their abilities, which may be the reason. If so, I'd like to see this changed, as it makes no sense if the actual spell still isn't able to instantly reveal stealthed creatures. In any case, I'm pretty sure that the above scenario was extremely unlikely if everything works as it should.
If you're aware of this and haven't planned on changing it, then consider this a suggestion instead of a bug report.