Two things may cause this problem:
1. you forgot to specify the top level module in the simulation, or use the wrong path. Just select the top level and try again.
2. it may be cause of the optimization somehow removes the name of the top level module. Find a file called "modelsim.ini" in the installation folder and change the line "VoptFlow = 1" to "VoptFlow = 0" to turn off the optimization option for simulation. It may slow down the flow a bit, but better than not working, isn't?