Never had this issue with my Janome 6600. What thread are you using? I cannot FMQ though I can do Piecing with Coats & Clarks all purpose from WalMart.
My tension is 7 pressure 1, feed dogs down, Mode 2, D01. Think long as it is a straight stitch it doesn't matter.
Clean the lint out, even under the bobbin case and up above the needle. See if thread stuck in tension wires above the needle.
Hope it gets better. I never had the problem you experienced but in learning FMQ I have my share of eyelashes on the bottom etc.. Good luck