I hope someone is coming along to help you. I don't know enough to know about the bobbin problem. 2 things I learned about FSL. I use 2 sheets of Vilene which is a cloth type WSS. I also slow the machine down to the lowest speed. Good luck

sukirani, I use two layers for WSS (Water Soluble Stabilizer) the material (mesh) look, not plastic look - hooped tightly in the appropriate sized hoop for this design. The same thread in the top and bobbin area, I don't change my settings on my machine - usually the designer has that all set up - I use a 90/14 embroidery needle. Good luck and hope to view your project soon. *4U shirlene

Yes, I agree with Shirlene about the stabilizer. In Australia we call it wss Vilene but, you have obviously got a Janome.
Keep using the blue tipped no.11 needles. You can use those for all of your embroidery, unless you are embroidering on fabrics like leather. I use it for fleecy and stretch knit fabrics as well.Don't use prewound bobbins. Janomes don't like them. Use the same colour and thread in your bobbin that you use on top for FSL.Have your tension on 2 and slow your machine right down to 400.
Always leave your foot up when threading the machine.
If that doesn't solve the problem there could be another reason.
Let me know if it does.
If not, I will explain the other reason to you.

What brand is the blue tipped machine needles that you use?

sukirani, it is recommended that you use only Janome or Organ needles with your machine because the shank is a bit shorter. Organ actually make Janome needles.