My modded Skyrim ran smooth in the past, but after I reinstalled my Win7, game begane stutter heavily. Its like random frequent half sec freezes even though FPS is 40+. Im using same inis and same Skyrim and ENB files. Maybe it caused Nvidia settings for my GTX 680 to drop and this was the cause? Please help

Check for background programs. You may have had some disabled before you reinstalled the OS.

Edit:

Just had a thought: the search indexing feature of Windows may be to blame if you had that turned off before. You may want to check on that, too.

in addition..... Read above too

Driver settings for your nvidia card will revert if you reinstalled everything. What happens when you get rid of all your graphic/texture mods? Disable enb, textures, meshes, sweetfx, etc and see what happens.

You can just rename the textures + meshes folder in Data to disable those.

Try as Deaths_souls say: http://www.addictivetips.com/windows-tips/disable-search-indexing-in-windows-7/

See if you have Vsync=adaptive in your Nvidia Control panel.

And see what background programs are running. !!! (disable those if possible), and try again...