Does it happen in one direction or another, and have you tried different places on the frame? Or is it all the time no matter what you do (circle, straight, etc.)?
My friend's long arm set up was rather fussy, the machine needed to be leveled and even though it was pretty much a brand new house, we couldn't get one leg to be correct without a piece of cardboard under it. The slight slope before we got the cardboard was enough to skip stitches if we were going that direction -- we could start that direction with no problems but not head into it.
Have you checked the rails and sensors? That sounds more likely to me that there is a ball of fluff or something that is going around and causing some sort of sensing issue.
edit: The other easy test if it is sensors is does it happen when you are unregulated? If there is a difference between being entirely freehand and having your stitch regulator going, that tells a lot!