Noticed something else today and what I'm hoping has fixed the issue albeit not convincingly.

Prior to installing GS I used to run a programmed mouse button that pressed F6-F12 in a step fashion while I held the button down.
When I installed GS cause I could put everything onto one action bar slot I changed this to just hit F6 over and over while I held the button down, delay of about 150ms between hits.
This is where I started having the performance issues.
For some reason switching back to the old F6-F12 spam corrected the performance issue, even though F6 was the only slot with a macro in it, why I don't fully know.
I then changed the mouse button to spam F6 four times (four was just a random test number) before delay and this seems to work for now too.

Seems messy and an unreliable fix and if it breaks again I'll report back here to let you know how I've gone.
As you suggested Bob, I'm thinking it might be hardware strain.

Thanks again for your time folks.