Hi Calum:
Well, I use the latest version of Firefox. My spyware protection is AdAware Personal SE, Spybot Search and Destroy, Windows Defender, AVG Anti-Spyware, and Spyware Blaster. I update and scan regularly. If it's spyware, none of them have found it.
It happens in all programs, though, for obvious reasons, it is very graphically clear when playing an on-line game which should have smooth, steady movement. For example, as I type this looking at the keyboard I look up every so often and see I have characters missing as though I missed typing them, but it is because there was a momentary freeze as I hit the letter(s).
Frankly it has been like this for many months and I can't pinpoint any event that seemed to precede it, sorry. I will look to update the Flash to the latest version, but I may have to ask you how to go about that, if I can't figure it out.