It could be your thread, it could also be your machine. Machines have 2 common bobbin set ups: Horizontal and Vertical. Most newer - not all - machines have a horizontal or 'drop in' bobbin. The thread has to turn a corner to form a stitch and on some machines it is almost impossible to FMQ on them. One noted for being unable to successfully FMQ with is the Brother Pacesetter PC-6500 (ask how I know) and there are others.
A vertical bobbin machine uses a bobbin inserted into a bobbin case. The thread path is straight up from the bobbin. Some machines like a class 15, a featherweight or a Singer 301, have the bobbin loaded at the end of the machine, others like Pfaff have the bobbin loaded from the front of the machine.
This is one of the many reasons most of us have several different machines!
I hope you get it sorted out, I'm sure your quilt will be beautiful.