Solved the problem. Basically the Macrovision FlexLM licensing software some how got messed up, maybe from the multiple versions of solidworks I had on the computer or something.
What I missed noticing previously was that when it was stuttering it was also at 100% hard drive usage and the fnplicensingservice64.exe was the root cause of it underneath ntoskrnl.exe
I fully uninstalled everything related to solidworks, the licensing manager and FlexLM / Macrovision including everything I could find in the registry as well. Then once reinstalling solidworks 2016 it's back to being smooth!
Hope that helps someone else!