How are you importing the files into Premiere? What does your folder structure look like at the OS level, e.g. how are the 3 cards save on your hard drive?
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My guess is that the missing files are the second half a spanned clips. They don't come in as individual clips as they're part of a larger whole.
The files are spanned over multiple cards. I do find all the footage as one large file but what I'm trying to do is just use one of those clips. If I need only a small clip then its a pain to always have to have the large clip formed over the multiple cards always be put on the timeline. With my old CS3 the cards all imported into premiere cs3 as their individual files. I guess both have their advantages and disadvantages. I'll get used to it. Just with there was a way to turn that automatic combining of spanned clips off and be able to import just individual clips in their original name that is on the card in the folder.
If you Import the clips instead of using Media Browser, you may get them individually. (Although there could be other side effects to that method.)