I just had the same problem. I backed it up on the laptop and let the Autoset do what it wanted to do. The next day's data was on the card so I guess all is well.
Aliens. I swear it is aliens.
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Well, no joy here in psycholand. Looks like there are about 6 or 7 files it changes each time you turn it on.
Oh well, at least it looks like it is back on track now. I think Zonk has the best idea to safeguard your data when you download it: lock the card to read only before you stick it in the card reader and unlock it again before putting it back in your S9.
Ok, it's a long shot. But I'll add my two cents.
Once a long, long time ago when I was a newbie and still using an S9 AutoSet and downloading data into ResScan, the computer that ResScan was installed on picked up some virus or other through the internet. The computer was mainly used for downloading my data into ResScan. And the only symptom was that every time I stuck the card back into my S9, the S9 choked on it and complained about an "incompatible card" or some such thing and the S9 would ask if I wanted to erase the card and re-format it. And (because I'd backed the data up to the computer) every day I let the S9 re-format the card. And the next morning the cycle would start all over again. The data would download to ResScan with no problem, but the S9 would squawk when I put the card back into it. This went on for several weeks as I recall.
At some point I did something else on this computer and go some kind of a message that indicated there might be a virus infection. And when I ran the scan, the anti-virus software did discover at least one (maybe more) virus on the machine. After disinfecting the machine, I never had the problem recur.
So---if it's been a while since you've done a full scan of your computer, it may be worth checking the computer out for any viruses, worms, or trojan horses. If you find any kind of infection, that may be the source of the problem. And once you take the time to properly eliminate anything that's found on your computer, the problem with the S9 not recognizing the SD card after it's been in the computer should go away.
Thanks for the suggestion...I'm running all the latest versions of my antivirus, anti-malware and firewall software and the scans are showing nothing of concern other than Flash and Silverlight (which seem to always be flagged with how tight my settings are just because of the coding they use). I'll try another sweep, but I think having the cards to read only will help with the potential for there being plug-and-play artifacts left on the card (which could be a source of the hiccup folks have from time to time).