You might try to tighten up your tension also. Just a wee bit.
I was trying to sew 2 pieces of flannel together the other day and mine would do the same thing. I did 2 things. Tighten up the tension a tad, and changed my top thread to a larger spool. Not sure which one was really the one that did it, but after I did both things, it worked just fine for me.
Good luck
Bev