PEP3 was released only as beta and does have some memory leaks that can cause file corruption. If you use it, save often and to different file names.
That being said, PEP3 brought about functionality to keep multiple XCF configurations in a single file, zip files (1+ XCF files) within a single zip file (MXCF). The second piece of functionality that was delivered was something called Overlays which were specifically designed to support firm keys on the in wall TSX9500 which does not have hard keys under the screen.
Unless you need to use overlays, I'd recommend you going back to PEP2.4.
To do this, you can simply 'export' your current config to a PEP2.4 compliant version using File->Export if I recall correctly.
This being said, one reason you may be having issues with remotes is that Windows Media Center uses an IR code format that by default requires toggle bits. If you would like to turn that off and give it a try, I would recommend searching the Pronto Pro Next Generation (Pronto NG) forum for the keyword 'debounce'. There used to be a windows registry setting that will disable toggle bits.
For multiple key combinations such as Ctrl + Alt + Home, for example or Shift + a for "A", you may find that you cannot learn these as you like.