You should always regularly backup the files on your media card. Media cards don't last forever. It also makes restoring the card easier. It only takes a couple of minutes depending on how many files you have.
You should definitely backup your media card if you are going to do any scans or repairs on it.
FYI, when I plug my BB into my work computer (Windows XP) and enable Mass Storage Mode the computer doesn't find errors in the card. When I plug my BB into my home computer (Windows Vista) and enable Mass Storage Mode the computer usually says there are errors in the card. I click on "Don't Repair" or whatever it says. My card works fine anyway.
--Ariel
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