strange. but i remember i had such a problem before.
are you sure you packed the .pk3 with ALL default zip settings? (e.g compression ratio,...)
i once had this come up, wouldnt have been able to find the problem, since the game finds the bsp, but cant load it.
only got to the bottom of this because a friend said he couldnt open the pk3.
so check your compression/packing setting in 7zip