I've even tried corrupting the cfg.txt file were is stores the current shot number. LFS repairs that line so you have really got something weird.
If it were me, and you may not be bothered to do this...
Re-install a fresh Demo version of Z28 somewhere else on your drive. Maybe a folder Called LFS1 or something. See if Ctrl+S works with it. If it does, unlock it, re-install all your mods/textures/settings/setups one by one testing ctrl+S works each time you add new things. Eventually you might stumble upon the problem causing it. If not, then delete the corrupted version of LFS and continue using the newer/fixed one.
PrintScreen should actually give you the best quality you can get, problem is that you have to save each screenshot manually or you will lose it. You can use Fraps to capture screenshots if you can't get CTRL+S working. By a chance, is there any background app running on your PC that might also use CTRL+S keystroke?