u must have the path wrong ,u might revise it but u wouldnt spot something like
c:\program files from c:\program flies .my advice would be to make sure the paths are right .right them again if necessary .
mohaatools could be installed anywhere u want ,even in the recycle bin (but that wouldnt be very useful

)
but all u need to do is put the right paths between the game and mohaatools .what actually happens is mohaatools searches for the pak#.pk3 files which have all the textures, effects ...other stuff..... .
so if u got a wrong path it would screw up everything (isnt it logical? )
also if u should be sure to make a different folder where all the autosaves and other compilation files .again all u need to do is put the correct path and everything will work as sweet as candy
hope that helps