I had a merged patch but I disabled when I disabled a mod that was a master to the merged patch. Even with a merged patch I still had the issues. And I've tried using the fake fullscreen that came with my enb, and that didn't seem to improve anything. Even when disabling the ENB the issues persisted.

And as for some specs:
CPU: AMD FX 6300 @ 3.5GHz
GPU: NVIDIA GTX 750 SC

Did you tried to use the wrye bash to make a bashed patch?

I've never used wrye bash before so no. I'll give it a try though

There's an issue with the TTWOptions plugin, make a clean save without it and update to the hotfix.

A newer version of it will be up tomorrow probably with some additional balance changes to the Bobblehead module.