What kind of FMQ foot are you using: gliding or hopping?
Are you quilting on something different than you usually do such as batik or a different weight of cotton fabric (bedsheet, tshirt, etc)?
Is the batting different than what you normally use?
Different thread than you normally use?
I have a Janome Magnolia 7318 so a similar machine to yours except it's mechanical. I love this machine but it really hates a gliding style foot. Anytime my machine doesn't have enough pressure from the foot, it doesn't like to form stitches correctly so if you're using a gliding one, make sure you have it set low enough? If a hopping foot, make sure it's lowering correctly?
People have mentioned before that they've cleaned out the entire bobbin area and then when they went back and checked again, there was a tiny thread stuck somewhere very difficult to see that was causing the problem? So maybe clean out the bobbin area again, re-thread, and try again?