Can MenuQue read from inside BSA's? That may be the problem. I made a BSA for RadarSystem. I'll test without the BSA.
MenuQue simply add many functions to edit the xml files during the game. Nothing else.
The mod (In this case Radar System) only have to specify which values and textures to use.
The files in the BSA are read by the Oblivion engine.
Maybe it can't read the BSA because you have to many of them. Oblivion support a limited amount of BSA.
If you have many BSA from mods, try to unpack the 2-3 smaller ones with OBMM.