So I upgraded to the latest pluraleyes today, I tell it to sync my footage and did the "replace audio" option, figuring it would save me some time.
And it did!
But for some reason, all of the audio is off by a few seconds. I pull it from the browser into a timeline, and FCP lets me know that the two are off... say, the video has a -17 and the audio has a +17. So, easy enough, I move them back together and they're synced. I put them back up in the browser so I can choose my in and out points to edit from... and they're back to being unsynced.