If memory serves, TOS, TNG and DS9 were initially released on DVD in hard plastic collector's cases (one per season) and spaced over a few years (don't remembering seeing VOY get this treatment). A few years later TNG, DS9 and VOY got a re-release in slimline DVD cases, with each season consisting of 4 packaged in a cardboard slipcase/box. Here in Australia, at least, each of the three series had limited-edition carry cases if you bought all 7 seasons together. There have been several other re-pressings since.

If your DVDs are all matching (e.g. from the same release run), then I'd be suspicious that it's the discs themselves or the cases (but you've said elsewhere it's not the cases, so...). Obviously it's an utter pain to back up that many discs -- 46 to 48 for each series, depending on which release you've got. If they're notably different pressings, though, then I'd think it less likely to be the discs themselves.