Have the same problem in FCP7. Found a work around:
1. Place Shogun files in sequence and delete first 2 channels of blank audio.
2. Export all the full Shogun files w/ just 2 channels as AIFs.
2. Delete Shogun files from sequence and replace with AIFs.
3. Sync in PluralEyes.
4. Replace AIFs in sequence with original Shogun files.