Same thing happened to me a few hours in. It was an eight player free for all with pirates and occurred even when there was nothing actually happening on the screen battle-wise. Most likely, for my situation at least, it probably means something with the CPU code is bogging down. In Supreme Commander, it was always the AI that caused the CPU to slow way down when there were thousands of units in the game even if they were off screen (meaning not graphics related). This always happened no matter how powerful your computer was also like Emjay86, stein220 and others have reported.
SupCom is 32bit and not multi-thread capable and only uses twoish gigs of RAM natively. In the case of SupCom: Forged Alliance, there was actually some kind of memory leak that the AI caused over time that would slow the game-time down to -10 eventually. For Sins, I could see how restarting the game may have fixed the choppy issue. If the game is having issues removing threads that don't exist anymore like from a destroyed ship or something then they could be building up over time.
I suppose when you have games like Sins and SupCom with potentially thousands of units needing AI commands at once and who knows how many threads trying to be processed this is to be expected; especially during a beta. The ultimate agonizing irony is that I decided to save in case the game crashed because of this and it crashed right when I clicked on the save button as if clicking the save button actually crashed my game 
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EDIT: The same crash just happened again on the same match the exact same way, but later in the game by about one to two hours. I was done playing for the night and went to save and boom! crashes to desktop with no errors. Odd thing though is that both times it has also caused major issues with Steam. Steam is still running but if the main window is open it will be "Not Responding." If it is minimized in the system tray then it won't come back. Clicking on it in the system tray does nothing and the only way to get it working again is to end the process and log back in. I'll try and get more info to try and pin this down.
EDIT: I also noticed that along with the horrible choppiness zooming in and out, there is also an input lag that usually makes your first left-click not register meaning you have to usually click twice to actually get it to recognize the click. The mouse pointer is moving without any choppiness at all though.
