I've used pause fairly extensively, but I haven't run into this. Maybe I'm just not leaving it on pause long enough. Hmmmmm.
I'm curious if it remains bit-perfect aside from the flipped channels, i.e. flip the channels back to where they're supposed to be and see if it matches the original file. I'm not in a position to do any testing at the moment - anyone wanna give this a try? If it retains bit accuracy even though the L/R are switched, it's easy enough to flip the channels in post production on the PC = IMO, not a huge deal. And if it doesn't, still BFD as I just won't leave the sucker in pause. It's just as easy to get it all set to go and just press Play when it's time, only takes about ~2 seconds to start the recording (still faster than starting a DAT recording that's not already in pause).