Corded or wireless mouse?
Wireless mice tend to do all sorts of freaky/annoying as hell things when their batteries start dying.
Currently I'm using my wireless mouse, though I've still had issues with my new wired mouse.
How often does this happen, and how long are each pause/skip?
I may have found a way to fix it although it's not the most desirable way to solve the issue, typically it will skip every half second to a full second of movement, whether it be up down, left or right, or in a circle. Strangely (for me, not sure about the others) it still follows the course that the mouse was told to take, the FPS for the game is always above 60 though so I don't think it's lag from that.
I fixed it by turning off pointer precision, it makes the mouse a bit more... wobbly? I don't know, it's just harder to move. I actually just typed it into google and here's the first page that I read. I think that I may have solved it, not sure yet
http://www.teamliquid.net/forum/viewmessage.php?topic_id=156685