Are you using a particular thread or is it all the time?
The Bernina my friend gave me she gave with the warning that it was pretty fussy about thread but seemed to like Aurifil -- which it does. It does ok with my left-over dual duty. I've been having issues with my machine quilting and this weekend I bought a light weight bobbin thread, Sew Fine by Superior to try.
I was able to use a friend's Pfaff P3 long arm set up for a couple of years. It was really fussy with threads and we couldn't wind a quality bobbin. Once we switched to pre-wound lighter weight bobbins instead of the same thread top and bottom things got better quickly.
Sadly, I'm finding that the skills I learned on the long-arm and moving the machine are not translating so neatly into moving the fabric at my large throat Bernina, but much better than with my old vintage machine with the feed dogs engaged. It's always something!