I have a Janome 8900qcp and have not had any problems with bobbins breaking and I have used my machine a lot both for stitching and FMQ.
When you fill your bobbins, especially with the clear thread, try using the on/off switch rather than the foot pedal to run your machine and set the speed on slow. The on/off switch is a more even speed than using your foot so the bobbin will fill more evenly. You don't have to worry about when it comes to the full point because the machine won't let the bobbin overfill. Just hit the off button when the bobbin stops going around.