No... your question might be a fit. But I really can't tell you the difference. And I kind of hoped, that someone else would take the baton and answer... :-)
Do you have more data points - like a) happens when transcoding only, B) with native played files?
This is strange now - I tried playing some files with "force transcode" set to on, and I wasn't able to pause. After that, I played with some settings (force direct play, force transcode) both on/off and vice versa and after that, I ended up using the same settings as before (direct play false, force transccode true) and everything is fine now. All files I tried until now can be paused and resumed.
Hope it persists, otherwise I will post here again.
But just for my understanding: Normally there is no limitation pausing and resuming files played via PlexConnect and PMS, this should be the normal behavior, right?
After reboot of the PC with PMS installed, the problem persists again. Maybe I try a fresh installation. The problem occurs with all file types, native and transcoded ones.