When i read your post, i immediately wondered if you might be experiencing this problem after using the automatic thread cutter (ATC) on your machine. It sounds like others have experienced that as well - including me!
I used to do all my FMQ on my Janome 6600 and have experienced the problem only when using the ATC function. I wasnt aware that maybe this problem could be remedied, so that is good to know! I got so frustrated with it that i quit using ATC entirely when actually quilting although i do still use it for piecing (still a problem there but the area is a little more accessible when piecing). My sitdown longarm (Nolting Quilting Bee) doesnt have this function and i actually dont miss it because my only experience with ATC was so frustrating!!! Please let us know if you come up with a fix or a work-around. 😊