I am sorry I can not help. I have had moments like that with my 6500 but it was usually something like the wrong thread. something I have been doing lately is NOT dropping the feed dogs, setting it to quilt mode 2 and then just quilt away. I get a more consistent stitch and less hasle. Have you tried replacing the needle or putting in a new bobbin? sometimes all I need to do is step away for a day and then I am fine again.
There is a list on Yahoo for people that have Janome 6600. Mine is its forerunner, Janome 6500. sometimes a mess on the back means tension issues on top. I have also had issues that my spray baste was jsut too much and goopie.
Also did you change your tension to close to 1?