When I had trouble with my card last January after it got cold when the OT was in its case in the trunk during a 90 minute drive in sub-zero weather, I had projects that would load without error but had the actual contents and settings changed. Mostly it was REC settings getting scrambled but I also had some pattern and part data disappear. Other projects did have files that gave me error messages when I tried to load and some were fine but most of them loaded like normal but were, essentially, partially randomized. Reformatting in the OT didn’t fix it and reformatting with Windows didn’t fix it, but using a low-level CF formatting tool (I linked to the two I tried here but I don’t remember which one ended up working; one of them would hang at 99% every time) cleared it up and it has worked fine ever since.
This probably isn’t your problem but if all else fails give it a try.