It sounds like you are not wrapping the thread into the bobbin winding spindle, on top of the machine. It is "spring loaded", to create tension, on the thread, as the bobbin winds. If there is no tension, on the thread, as the bobbin winds, it will cause the thread to wind loosely. This is why you have a certain amount, of success, by using your finger to hold the thread, thereby creating some tension, on the thread, as it winds.
My machine is a Kenmore, which is made by Janome, so it is not exactly like yours. However, I am pretty sure, that all Janome machines have the same type of tension spindle on top, of the machine, for keeping the thread tight while winding the bobbin. I just checked my machine, and there is an adjustment screw, going into the tension spindle, which allows for tightening or loosening the tension. If you are using the tension spindle, it may need to be tightened, with the adjustment screw.
You are probably right, that the loose thread on your bobbin, is the cause of your bird's nests on underside, of your stitching. By tightening the tension, while winding your bobbin, this should resolve the bird's nest problem
I hope this helps. Happy sewing . . .