No wishing to hijack this thread but I am having a similar problem. I have W7-64, PPCS6.0.3 and am trialing Pluraleyes windows version with PP plugin 2.0.7 (8433).
I am trying a real simple test, GH2 MTS clip with camera sound and Zoom H4n WAV for close sound. I put the WAV below the clip on the sequence, nothing else on the sequence and via Extensions run Pluraleyes. The returned sequence puts the WAV at the start of the timeline and the clip after it. So totally out of sync. Sound on camera clip is ok to hear the same audio as recorded on the H4n but pluraleyes does not even recognise the sync audio.
So simple sync not working for me either.