I'm not surprised you have CT thread in the bobbin which is a 3 ply 50 wt cotton and you are trying to quilt with a trilobal 40 wt poly in the top that is a weak thread to begin with. Rainbows (as well as it's sister solid, Highlights which has been discontinued) want very loose tension in the top as per Superior:
http://www.superiorthreads.com/reference-guides/ Click the hyperlink for Longarm thread reference guide. Notes for both these threads state: [TABLE]
[TR]
[TD]Loosen tension settings as necessary
[/TD]
[/TR]
[/TABLE]
I recommend changing bobbin thread. Either wind your own bobbin with the Rainbows or go for a lighter thread in the bobbin (ie a 40 wt poly or lighter) So Fine or Bottom line would be good choices if you don't want the same thread in the bobbin. Additionally, if you run Essential cotton a lot you may have a blob of lint caught in the tension spring of your bobbin. Take a fine pin and run it under the spring to dislodge any blobs of lint.
Essential cotton is ok to run in the top but I would not run it in my bobbin at all. It is just way to linty which leads to tension woes.