Im afraid that i don thave my books with me right now so i cant post a page number but as far as I know prestige classes do not count towards xp penalaties.
The 3.5 DMG no longer lists an exemption from multiclass penalties for prestige classes. That said, this omission has been stated to be an error by developers; this will presumably be in the 3.5 errata, if and when such a document is produced.