There's no doubt, you have to watch the mods and your VRAM usage. After removing all my grahical mods it's running like a dream, everywhere. VRAM usage is well below the limit for my cards now (where it was constantly on the limit before) so I'm sure it's that. I can even run lots of SSAA now. 
I think I'll add my favourite mods one by one and see how I go, and I'll probably try that light version of Skyrim HD too.

I think I'll add my favourite mods one by one and see how I go, and I'll probably try that light version of Skyrim HD too.

