When I import a MXF file from Nanoflash to CS5, then put the clip on the
timeline, identical audio pops up in audio tracks 4,5 and 6, but none in
track 1. Can someone explain this, and say how to stop it? Clips from
other sources behave properly.

If the format of track 1 is different from the format of the imported audio (e.g., 1 is stereo and the import track is mono) PPro will create a track in the proper format. You could change the format of track 1 to match before importing. That's the only explantion I have, perhaps there is another...

select the imported clip(s) then right click them and change their audio channel mapping to suit what you want, and as the other person stated, the tracks don't match. you can always do a "remove unused audio tracks command" to get rid of the topmost traks with nothing in them