I’ve never had this specific problem but for a while I was having issues with parts moving around, pattern data changing and record settings changing between power cycles, but with the current project and when I saved and reloaded. I’d also occasionally get 10-20 seconds of really nasty buffer underrun type distortion during playback from flex machines if the OT had been powered down for more than an hour or two.
Reformatting the CF card from a computer using a dedicated CF formatting tool solved all of it, and it seems to have been related to temperature - all of it started within a week of having to drive for an hour and a half with the OT in a hard case in the trunk on one of the coldest days in a decade, so it was easily -20c in there, if not lower. Most consumer grade CF cards aren’t rated for less than 0c. Apparently it messed up the CF format in such a way that most of the data was still readable (I did find a couple of corrupt files eventually) but the OT wasn’t loading the file structure of projects correctly so things got kind of jumbled up. Doesn’t sound likely that it would manifest this way rather than just corrupting files, I wouldn’t believe it if it hadn’t happened. No idea what the distortion was from, but all of it has been fine for over a year since the reformat.
Reformatting in the OT itself or with Windows’ built in formatting functionality did nothing, I had to do a low level format with one of the dedicated CF formatting tools that are floating around, I forget which one.
Probably not the source of this problem but if all else fails try backing up your data and doing a low level format of the card and then start a NEW project and see if the issue comes back (just in case the old data is corrupted). Couldn’t hurt.