Sorry I do not have a solution for your problem. But just to add that I'm also having the same problem with my Janome 6260! Irregardless of what tension I use, the bobbin thread always shows on the top. So yes, I do suspect this is the problem with Janome machines too. The funny thing is, when I brought my machine to the service centre recently, I highlighted this to them, they put the tension on auto and it was okay! Really, really weird....as it doesn't work at home for me. The saleslady however, did mention that it's sometimes due to a faulty darning foot.
I would like to hear too what solutions fellow forumers have on this issue.