Just a thought here, and maybe not the issue, but let's get this out of the way first.
When you Import your multiplexed AV files, PrPro needs to Conform the Audio. This can be almost instantaneous, or take a while, depending on the specs. of the Audio, the Duration of the files, and the speed of ones computer. See this article for more background: http://forums.adobe.com/message/3892177#3892177
It could be that you have allowed time for the first file to Conform completely, but began editing, before the others had.
Good luck, and hope that it's as simple as allowing enough time for Conforming of all files.
I've always been impatient I give it a try tomorrow and let you know if it is the problem.
Thnks so much for your answer Bill, they say patience is a virtue and it certainly worked, thanks again