the Polymorph subschool grants you a +10 to Disguise checks. Is this a +10 if and only if you are using Polymorph to attempt to appear as a specific individual, or is it assumed you make a Disguise check with each Polymorph in order to actually appear as the creature you are becoming?
(In essence, if I turn into a dog with a polymorph spell, do I automatically appear as a dog, or do I need to make the Disguise check to not accidentally make myself look half-pig?)
The way I run it is that if the perception check beats your polymorph enhanced disguise check they notice something 'not right' about you. How much information they get is up to the GM and probably their familiarity with your apparent form. Perhaps you didn't get the appearance quite right.