A couple of days ago I ran a CHKDSK and left it running for hours. When I came back it was stuck at about 95% and it made no progress for 15 minutes. So I did a hot reboot and cancelled the CHKDSK when it rebooted.

Now I'm getting some strange popups in my task bar, things like "Adobe Flashplayer $/Secure.exe is corrupt" and "TESV.exe is corrupt."

After I had rebooted I noticed that Steam was not happy staying in Offline mode and I had to actually verify the game from my library. The game launched fine from the SKSE launcher after that, and nothing seemed to amiss, except that old save files started appearing in my C:\Users\Anthropoid\Documents\My Games\Skyrim\Saves folder.

I played quite a bit bit last night, and saved every 5 to 10 minutes. When I was done I did my standard convention and moved all but the most recent .ess and .skse files to a C:\Users\Anthropoid\Documents\My Games\Skyrim\Backups directory.

When I played this afternoon, no problems. But then I went to lunch and put the machine to sleep. When I got back, and attempted to launch Skyrim using the SKSE shortcut, I received an error. Going into Steam online mode fixed this, and the game would launch. I played for a while, saving as I went, and accumulating about ten pairs of .ess and .skse files, then when I quit the game did the standard thing I do: cut all but the most recent from the Save directory and put them into the Backup directory.

However, when I next launched the game, the contents of the directory were from before I went to lunch! About an hours worth of gameplay comprising about 10 pairs of .ess and .skse files seem to have just vanished.

Any ideas what is going on here or what I might do to fix it?

Well it seems to have "fixed itself," else it is just not happening again yet. I suspect that it has something to do with Steam and something not working correctly when it is in Offline mode.

It probably sounds like I just made an error, but I swear to Arkay, I has played for about an hour, saved 6+ times, could see the list of saves in my in game window. Quit the game and they were just gone.

Glad you fixed it...

Actually, not fixed. I managed to replicate it this morning. I suspect it has to do with problems going on between SKSE and Steam, problems which I may have created when I aborted the CHKDSK, or which may have to do with changes to Steam.

Last night I put the machine to sleep having left one save file (#590) in Breezehome. I left Steam in online mode. Got up this morning and loaded the game from my SKSE launcher short-cut on my desktop-> game launched just fine.

I played about 30 minutes, saving once, then played a bit more. When I went to save a second time this is when I realized the problem persists: There was only one save file listed in my list of save files in the in game "Save Game" window. Saves were not actually saving, probably just as they were when this problem hit me yesterday. Yesterday I probably thought I had saved multiple times, but I was in such a trance didn't notice that there was only one file listed in the list every time I "added" another save file.

I quit and restarted the game a couple of times and confirmed it persisted across multiple sessions.

Launching Skyrim from the Steam launcher fixed it. I was able to add save file #591 and load it in game and it worked.

So, if no one else is having this problem, I guess it might just be things that have got messed up on my machine and I'll consider reinstalling SKSE to see if that fixes it.

Do that, verify your game cache files through steam, and run a CHKDSK too. (But this time let it finish)

Also you may wanna dιsable sleep.