I had the problem recently, the game didn't want to launch my Local Disc/Users/Username/My documents/My games/Skyrim saves because after the crash my pc created some weird Profilename and the game was running from Local Disc/Users/Weird_profile/My documents/My games/Skyrim I just copied the saves from one to another.

I also highly suggest backing up your save files, almost lost my 52 assain

I'm very frustrated with this game! When I first installed the game via Steam on my PC I was able to reach level 40 over a week before the game crashed one day. It was due to a cooling problem with my video cards. I opened the PC side panel and the over-heating problem was resolved. The problem was that all of my saved game files were gone. GONE! I have no idea what happened to them or how they were deleted but I was not responsible for the situation. I then started over at level 1, making sure to save a copy of my game files to a separate location just in case the files disappeared again. This time I reached level 48 without any problems and the game saves were copied. Today, I went to play the game after a reboot of my PC and the game files were gone again. Like I never played the game before. Plus, now the game will only load on 800x600 resolution as a small window on my display. Tried to start a new game and copy the old saves into c:/My Games/Skyrim location but it does not seem to access the copied files. Now it appears that I have to start all over again and I can't get the game to play full screen on my 40" display anymore. This is not my fault! I am not trying to play 2 characters. My files should not erase without my consent or knowledge. The game resolution should not change if I did not change it.

Did your entire system crash, or just the game?

Also try placing the Saves in \Steam\steamapps\common\skyrim\Skyrim\Saves (create this directory if it doesn't exist). Also place your INIs in the skyrim\Skyrim folder too. If that doesn't work, make \Steam\steamapps\common\skyrim\Saves and try placing them there.