You had something running in the background. Always check your processes via Ctrl+Alt+Delete. Depending on which version of Windows you're running, you can shut most of those processes down. If you aren't sure of one, just Google it.
One culprit is often an antivirus updating in the BG. For instance, Avast will cause intense system/Internet lag when its updating.
I don't think its Sins related, since I can play Rebellion on my Acer Aspire One Netbook without any lag at all till very late game on the biggest maps.
(Good job devs )