When compiling libraries for ModelSim from ISE 8.1i SP2, the modelsim.ini file is not updated with the new library locations if a modelsim.ini file is already in that directory.
This problem occurs with CompXlib when it is trying to map the libraries.
The problem appears to be intermittent.
This issue can be worked around by doing the following:
Deleting the modelsim.ini file that already exists in the directory.
Opening the modelsim.ini file in a text editor and changing the paths manually.
Use this method only if the modelsim.ini cannot be deleted.
Xilinx is currently investigating this issue.