I swopped back to the old header as well last night and it is now doing the same with them.
The "new" one's are OEM headers I got from a bandit V. I know that my emultion tubes needs replacing but the bike was still going ok as was. I will now just buy new gaskets as I kept the old ones. Don't really think it is the problem as there does not appear to be any blow outs. After riding a block it really starts sounding like the bike is intermittantly running on 3 cylinders. I'll probably just pull it in at a local shop to have the carburation checked quickly. Just odd that this started showing up after changing the headers. O yes I also washed the bike. Not that, that has ever been a problem.