Could be totally unrelated & don't want to scare you: but this is what mine was doin on the S2 a while back now. It was traced back to a plug which was rusting up, and ran lumpy until it had 'burnt' the rust off & ran fine. The cause? Head gasket leaking water onto the plug: when the engine wa hot tho, it evaporated any moisture in there & so only showed u pfrom cold after it had been stood for a while & the water had got onto the plug. Result= Rebuild with head skim & no problems since.

Check your plugs from cold & have a look at them. If it's rusty then there is water getting in. If it isn't rusty, then could just be some new plugs needed...I hope it is just the plugs you need mate.