When my machine doesn't move smoothly I first check to see if a cord has caught on something, but you've probably already checked that out.
I had a similar problem once, probably not what you're experiencing but I'll describe it anyway "just in case". My frame had "settled" over time, and the front and back rails were not equidistant across the full 12 feet. When the carriage approached the area where the rails were furthest apart, the machine kind of stuttered on the track. Then when it moved over that spot to where the rails were closer together everything was fine. I learned that Innova had slightly changed the frame design over time to put in more of the slats that keep the frame from spreading. I bought two more of these slats, installed them on my frame, and the problem was solved. I also found out recently that the dealer who set up my machine set up my carriage for a 22" rather than a 26". I don't know if that also contributed to the problem.