... but the contents do go into the regular windows cut/paste buffer.
This should not happen. PEP uses its own clipboard for storing pastetext. This done purposefully to avoid overwriting the global clipboard contents. That would be bad manners and a security breach (i.e., storing passwords, etc. that can simply be pasted into any application form).
Do you recall if the global clipboard contained any PEP pastetext when PEP was working properly? I've tested it on my system and it works as expected.
This may be a clue as to why PEP stops working for you. I still wish there was an easy way to consistently reproduce the problem so I could debug it.
Do you have any other extensions installed that place content on the clipboard? There may be a conflict. Perhaps you could provide a list of your installed extensions. If you have FEBE
installed, you can get the list by clicking FEBE Options > Advanced > List installed add-ons