Thought this could be useful if anyone encounters the same issue as me.
When I got Assassin's Creed it initially ran very well. Recently it had been pausing for up to 5 seconds, usually when you make a kill or collect a flag etc. I was baffled at first but a bit of googling found me a fix.
Disconnect the internet or block the assassins creed exe with a decent (not Windows) firewall. I was amazed. Simply unplugging my ethernet sorted the problem. I dread to think what the game's started doing in the background that it didn't used to.
The game is in dire need of another patch. I have to Alt Enter in just to get it to run in full screen, the exiting process is rediculous, and now this. Oh and it only recognises Wired not wireless 360 controllers by default. Rediculous!