All the pros I know reformat everytime they put a new card (that's new from the box, or new from the card reader) into the camera, and do the re-format in the camera. It does clear up the index files, and cleans out the stray junk that simply deleting leaves behind, and prepares the media for whatever device is going to record on it. Before I knew about this, I found myself getting fewer and fewer images on a card, because, like de-fragging a hard drive, there were pieces of deleted files all over the place (remember, delete doesn't really mean delete. Format means delete). I'm sure the real techno geeks can explain better than I, but just do it. I can also tell you that I could never get files to download from a card reader, until I bought real Firewire cardreader from Delkin. Those cheapo readers that come with some cards never worked for me, so I was always downloading from the camera, which took forever.
Andy Pearlman Studio