In the mind flayer dungeon in the underdark, certain doors can only be opened by mind flayers or if you've turned into the slayer. What puzzles me, is that if you cast limited wish and ask to be able to turn into anything, then use the shape shift ability to turn into a mind flayer, you still can't open the doors. Is this just one of those quirks in the game, or is it that my version is buggy?

It's one of the quirks in the game. You can potion up to 25 Intelligence and... cannot open the doors. You can Potion/Draw Upon Holy Might or the like up to 25 Stregnth and cannot open up the doors.

Where as you should be able to open up these doors if "Godly Might and Powerful Mind" needed... dialouge is accurate. So it's no suprise that your transformation into a Mind Flayer wouldn't work either.