First ... what kind/wt thread are you using in the top and bottom?
Second ... describe 'rats nest'. Are you getting it just at the starts, all the time, on curves?
I don't have the same machine, but on my machine I don't always have to change the top tension when I move from sewing seams to quilting (FMQ or otherwise). I make a test sandwich first, check my stitches, and if I have to change the tension at all it's usually only 1 position. I've never touched the bobbin tension.
Also, when was the last time you changed the needle, and is the needle the right size for the thread you are using. And, have you tried completely re-threading the top of the machine?