These are the ideas for the `simple things' that might go wrong:
You can use ldd(1) to see which dynamic libraries an executable links against (although I can't see exactly what you'd use this for in your situation, you might find a use for it). Check that libPEPCF90.so.3 exists (using locate, find and/or ls). Check that ld(1) will actually link against it (i.e. check that LD_LIBRARY_PATH is properly set, with ($ echo $LD_LIBRARY_PATH)).
What I think might
have happened is that the new versions depends on different libraries than the old one (use ldd to compare), and you don't have the correct libraries (however, I can't figure out how that can happen with a sane package manager
So, my question for you: what is the results of your findings?