I'm don't use PluralEyes, but the Canon MXF files I use are interpreted as dual mono. I just click on the clip and interpret the audio as two channel stereo. Maybe that will work for you?
From that page:
You can apply the Modify Clip command to a mono clip only in the Project panel, before the clip appears in a Timeline panel. You can’t convert a clip instance to stereo when it’s used in a mono audio track.
Unfortunately, that will not work for me because once I import the XML all the clips are already synced within a sequence. Interpreting the footage is only an option via the project panel before editing.
I have the exact same issue and I use Pluraleyes3. This is also a dealbreaker because omf exports won't work, it seems to hang at the first instance of a file jutted to two mono tracks. I have Premiere Pro 5.5. I've been trying to figure out this issue for several months. My sound guy is also baffled as to why it happens.
I suppose this is most likely a PluralEyes issue and I'll be posting over there (although I have to say RedGiant's user forums aren't as 'robust' as Adobes.) But if there were a workaround in Premiere that would at least help in the interim.
snoshreddax21 did you find any workaround?
This is most probably a Final Cut 7 XML legacy. As far as I understand, PluralEyes just esports kind of FCP7 xml into Plremere (which is of course edible by Premiere), however the stereo tracks are being split into sort of a1a2 the way they would be in final cut.
That is a huge pain for me as well. Looking for a workaround.