The workaround I use is pretty quick:
1. After Pluraleyes has finished syncing, open the timeline in Premiere (I choose the timeline where Pluraleyes has synced audio and video but hasn't replaced and cut up the audio)
2. Replace the full synced audio clips in this sequence with the original full source audio clips from your project (they have the same name - just be careful not to use the ones imported via Pluraleyes).
3. Start editing. Apply audio filters as per normal.
The problem seems to be with the audio files imported via XML.