Looks like this problem may be individual hardware dependent, although PS Audio tech support never suggested I return the unit so that they could swap drives and see if the problem persists. They just told me its a known issue and I have to live with it. Well, maybe I will and maybe I won't.
If you use the "stop" control the problem does not exist. But then you cannot go back to where you were when you were interrupted.
I have no quibble with the sound quality. But I recently acquired a Bryston BDP-1 and A/B'd the Bryston vs the PWT and I could not hear a difference. That was with a ripped .wav file using IMGburn and a Plextor drive, so the rip was not technically a perfect rip like you may get with dBpoweramp. I used the identical CD for both the rip and playback in the PWT. And when you pause the Bryston, you can replay without a hitch.
Although there is a bit of a learning curve to use the Bryston and you have to spend time ripping your music, sonically they are extremely close. If you are going to listen to single CDs, then you can rip a CD and put it on a USB drive in minutes and be listening almost as fast as loading the PWT. Plus, if you want to put together an afternoon of listening with three or four albums, the Bryston can do that easily and the PWT cannot.
Perhaps for some the sonic edge may go back to the PWT if you use the PS Audio DAC. I am using the Bryston BDA-1.