I have not read this whole thread so don't know if someone already told you, but I've had the same problem with my Janome 6600P many times. Last year I finally took it to the dealer, cause I was going nuts with this problem. They helped me to analyze what was going on. It seems like a bobbin problem, but it is really a problem with the upper area of your threading.
Although I initially threaded it correctly, sometimes, (for an as unyet determined reason) the thread hops out of the silver thread take-up lever and goes directly from the tension regulating dial down to the needle area. Simply lift the foot, and totally rethread the top of the machine to solve the problem. One thing they told me to do is listen for the little click as the thread enters the top of the silver thread take up lever. There is some little tiny mechanism there that is supposed to help the thread stay in that arm as it goes up and down, and indeed, you can hear it click as the thread passes into the slot on that arm. I've found that now it still happens, but I at least know what to do to solve the situation.
I love my Janome now, even with its idosynchronicities, and hope you have great luck getting on top of this issue to love yours as well.