Yeah, the only exception to the Modified Game rule is music packs, iirc. Even graphics packs trigger the Modified Game rule.
Also, a tip for ya: If you want to check if you've modified the game at all, type "ISGAMEMODIFIED" into the console. It'll tell you if the game is modified and if you can unlock unlockables. (ie: Say if you have the Mystic Realm loaded, which uses it's own data files.. it will say that the game is modified, but you CAN unlock secrets with the WAD)