Which profiler do you use for Fortran code base with MPI in it? gprof doesn't seem to be working correctly. Sun Studio Analyzer only returns the timings for the C/C++ system calls and none of the fortran functions appear.
There are a number of performance analysis tools specialized for Parallel/MPI Programs, such as:
At first they may not be as simple to use simple to use, but they provide much more help to investigate the performance of parallel applications.