File won't import due to 'Too many audio channels'

I've managered to import one 30 minute video recorded off a screen recording program off the AppStore called ScreenRecordStd. This software has an 'include computer audio' button which I activated after the first 30 minute video.
Once trying to import any videos with this selection activated they won't import, telling me there are too many audio channels.. so I know it is due to this selection. The file information tells me I have two AAC 44100 Hz Stereo files as part of the video, when I change it to mp4 or h264 file formats it does import but the video/audio are not in sync when played through on Premiere Pro but are totally fine in QuickTime player.. also the second audio channel is a lot quieter when being played through on Premiere Pro than in QuickTime.
So, I hoping someone has came across this software or this problem and can help me. So I have two 44100 Hz stereo files within the video and the selection I am using says it can take up to three stereo files, so why is it telling me it can't import because there's too many audio channels??? I've tried changing the video to h.264, mp4 and they just struggle with the video being too slow and avi. just has the same issues as .mov.
Can anyone help?
Thank you.

Why do you convert the media to start with? Are you aware of that you are converting the camera's MPEG2 to the MPEG2 you get when creating the new MXF file? (XDCAM HD = MPEG2)
I would never ever re-compress/convert the already-in-camera-compressed MPEG2 to compressed MPEG2 for editing and then having it to end up in let's say either MPEG2-DVD or H.264. You loose one generation and i would not want to lose it by re-encoding to MPEG2 since, imo, re-encodong MPEG2 to MPEG2 should be avoided. (MPEG2 to MPEG2 = The quality is degraded too much) If you still want to re-encode the footage i would use another codec, DNxHD/CineForm/Lagarith. (Pick your favorite)
You can use the MXF files from Canon XF Utility in CS6. (The files MXF are just copied from the original folder structure, so no re-encoding is done.)
AFAIK, the problems with tearing video go away by using the MXF files you get from XF Utility. If the tearing is still present, close Pr and delete all Cache files. Open Pr and let the Generating Peak file finish.
AFAIK 8 audio channels are standard in MXF OP1a according to SMPTE D10.
/Roger

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