You have a ton of useless crap in there, and having too much in your autogen can cause it to reset. To fix this, delete stuff that isn't necessary. For example, the pop-up lines for Relic mod. You can delete those. For that matter, you can delete any settings you haven't changed. When you open Trem it should auto-re-add the ones you delete with default settings.
As for Sprint Toggles, leave it off. It's better that way. WW Toggle is another story. To fix that, add "cg_wwtoggle 0; cg_wwtoggle 1" to the top of your autoexec.cfg. Your autoexec.cfg should also include your binds and settings that are currently set to non-default values. That way, even if your autogen gets written over, next time you start Trem or do /exec autoexec.cfg it will be back to your normal settings and binds.
For cg_shadows 2, I see no reason for your problem. Try adding it to your autoexec.cfg, and see if it works then.
