Another user reported a problem with Fragpipe which was happening because BiblioSpec was trying to find the spectra in the .d raw file folder, but the spectrum identifiers in the pepxml only made sense if you were to look for those spectra in the .mgf file.
Here's the support request for that:
I am not sure whether that might be the same problem that you are running into. If it is, the workaround is to make sure to delete the .d folder, and any .mzML file that you might have in the same folder as your pepxml file, so the only thing that BiblioSpec is able to find when it goes looking for spectra is going to be the mgf file.
This other user described the problem as a hang because it was taking a very very long time to not find the spectra in the file it was looking through. However, I could imagine the behavior could also manifest itself as no spectra found.
If that does not fix your problem, then you should send us your files and we can try to reproduce the problem.
You can zip up your files and upload them here: