Syncing Shogun Footage with PluralEyes? I can't get my video footage to sync with my audio in PluralEyes 3. Here's what I tried...

I shot some interviews today using a Sony a7s and Atomos Shogun. I recorded almost everything through the Shogun but then my battery died on me and I recorded the last few clips just through the Sony. For audio, I recorded from a Sennheiser boom through a Zoom H4n.

I imported everything into Premiere Pro and made 2 sequences: one for the Shogun footage and one for the clips just recorded on the Sony. I sent the Sony sequence to PluralEyes 3 and it synced fine. But when I sent the Shogun footage to PluralEyes 3, it wouldn't sync. I tried importing the footage straight to PluralEyes (instead of sending it from Premiere) and that also didn't work. It won't sync at all; all the clips are red.

I double-checked that the Shogun recorded audio and it did. It recorded 4 channels, but 2 of them are silent. The H4n recorded in stereo (just in the left channel though).

Has anyone else experienced this problem? Any suggestions on how to sync my footage?
I am on Premiere CC 2015, which has its own PluralEyes equivalent for synchronizing audio under the "Merge" function. (I think it was also on CC 2014 but I am not sure what version originated audio sync functionality.)

Select your two clips in your bin and merge them (it's under "Clip"). In the menu, under "Synchronize Point" choose "Audio" and make sure the "Track Channel" dropdown is set to a track that has audio on it. The Shogun material I was using had audio on track 3.