That is what happens on my Janome as well, so I bought a used Bernina for FMQ and that solved my problem.
I know it won't solve your problem today, but I hear that machines that have a front loading bobbin do better FMQ work than those with a drop in bobbin. Most Janomes have a drop in bobbin where as Berninas have a front loading bobbin.
The positive in this is that the stitches should be easy to take out. And if it helps, I did the same thing on a twin size quilt one time and had to take out all of the stitching. Been there, done that. {{{hugs}}}