USER LIBRARIES (Quartus II 5.1/7.2)

For Quartus to find a file in the library directory, the filename must match the entity name inside the file.

I think two entities with the same name was the situation for which I filed an enhancement request quite a while ago. I vaguely recall that the change has been made by version 7.2, but I don't know remember the details and so don't know whether it covers your situation. It might have been a case where two different VHDL libraries contained the same entity (not quite the same thing as a Quartus user library).