Audio problems importing Supertintin files

We use Premiere Pro to edit small videos as part of our work, but none of us are professional video editors. We've been recording Skype interviews with Supertintin, which produces MP4 files.
When we brought these into PP, we were getting horrendous audio drift, so we got Aunsoft video converting software as recommended by Supertintin. Converting the MP4s into MOV files before importing seems to fix the audio drift problem, but it brings in the stereo audio tracks as 5.1  and puts them into audio track 4.
Is this a problem and are we doing something wrong? Thanks!

I came across a similar problem with a video with 2 video tracks... the following worked for the video tracks (but no guarantees it's the same for audio.)
Try this:
Import the clip into FCPX -- for now, don't transcode anything (uncheck everything in the import dialog).
Once the clip is in FCPX, right click and select Open in Timeline.  See if both your audio tracks are in there. The overdub might be disabled (if it's in there.) You should be able to switch them by selecting the French track and typing V, and re-enable the English track by selecting it and typing V.
If you have Quicktime 7 Pro, you can verify if all your tracks are included with the video by opening the file, typing Command - J  to open the Properties dialog. You should see a table with columns Enabled, ID, Name etc. -- the Enabled column is a checkbox. The ID will usually be a sequential value for the track number and the Name column will be something like Video Track, Sound Track, Text Track, etc... so you can identify which track is what.
I'd hold off merging audio tracks until you figure out if you actually need to or not. At worst, you might have to export two different versions of the video.

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