What if you save manually ???
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Do you have mods, what's your computer specs ???
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Diable Steam Cloud. !!!
1) In your Steam Library, right-click on Skyrim and select "Properties."
2) Click the "Updates" tab.
3) Uncheck "Enable Steam Cloud synchronization for Skyrim."
4) Click "Close."
You wanna Turn off Steam Overlay. Steam overlay is a in game overlay that allows access to steam communities in game, as well as the ability to take steam based screenshots.
Turning this off can also help with issues whilst using some Enb's, such AA not working and bad texture shimmering.
Also known issues involving the Steam Overlay include a drop in the game's performance or frequent crashing back to the desktop. Disabling the Steam Overlay will help solve that problem.
In your Steam client, click "Steam," followed by "Settings." Navigate to the In-Game tab and uncheck "Enable Steam Community In-Game." Click "OK" to save your changes.