Does yours look like this one? I have a Janome 6500 and I've had some issues with this bobbin holder and replaced it twice. Its held by a magnet and can be dislodged during a jam up sometimes.
Have you taken the bobbin holder right out and cleaned underneath it? There might be a thread bit stuck in there that keeps causing the jamming. Take a look with tweezers and a torch and see if you can find anything in there. Also, is the bobbin holder itself damaged, look for burring and damage to the black plastic from the needle. (if there is some, try to just file any rough edges off with a nail file gently). Or buy a new case about $35 or so if badly damaged.
If you have never removed the bobbin case, then check your manual for instructions, or take photos as you go so that you can get it back in okay.
To get it out, you need to do the following. Unplug the machine, and remove needle plate, pressure foot and needle so you've got a good working area. Now turn the flywheel towards you so the rotary hook rotates while holding the metal back bit of the bobbin holder and pull it up towards you. At a certain point, it will lift up and out easily.
Clean underneath thoroughly using your little brush and tweezers making sure you take the lint or thread out of the machine area, don't blow it further in with compressed air.
Clean the bobbin case too and inspect it for any damage caused by the needle striking it when/if it has dislodged.
If your machine has a hole in the middle of the bed under the bobbin case, there is probably an oiling wick in there, give it a drop of good quality machine oil if you like, especially if you don't take it to the service guy each year. Not in the manual to oil newer machines but if there is a wick, you can certainly give it a top up.
Now put the bobbin case back in reversing the process. Your machine may have a pair of red markings on the bobbin case and the bobbin stopper that you line up. This is important, you need to get it back into the right spot.
On mine, during my last service, the tech fitted an extra little metal stopper from Janome which stops the holder moving out of position and seems to have resolved the issue. Mine would always jam up when I was trying to sew just a bit too much thickness of fabric so probably operator expectations causing the jam!!
I hope that I've helped out a little. If not, then perhaps take it to a serviceman and see if he has an aftermarket "part" for this model too, it has made the case on mine less likely to move out of position.
