Well, for one thing, you shouldn't be importing directly from the cards in the first place. You lock the card, copy the files, and backup the files to two extra locations before you start messing with importing. Before you do anything, do that first.
Second, the #1 cause of failure in Log and Transfer is that the user messed with the file system. Did you delete any items -- including empty folders -- from the card? This is also why you shouldn't import directly from the card. With tapeless camcorders, anything you want to change on the card, you must do it with the camcorder itself. Mounting a card via a camera, and then messing with the files on the card itself, is an extremely dangerous practice akin to unwrapping your 35mm film negatives and showing them off to the sun.
If the card is indeed flawed, if you can copy the contents off, there are alternate solutions if you can get at the actual MTS files. Voltaic can convert MTS files without the file structure intact, and I think ClipWrap can do it as well. I've only used the former.
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