On the issues with the pyfrm export from pointwise, I am assuming that pointwise haven’t updated there PyFR support since we added linear elements. This causes a few changes to the mesh format.
I recently had a similar issue when re-partitioning an old pyfrm file, I made this modified version of pyfr GitHub - WillTrojak/PyFR at feature/old_part which added some exception handling. That might help, or at least point you in the right direction to solve this issue.
As to the gmsh problem, are you using high order surfaces and periodics BCs? If so take a look at this High order curved mesh visualization - #10 by WillT
I think this might be your problem.