I do find flannel backings more challenging to FMQ than cotton. I find it helpful to use the teflon "Supreme slider" mat on the bed of the machine to help move the quilt smoothly. I also found myself needing to take more breaks as the quilt can be heavier. If you like gloves, they may help too. Flannel can sometimes be more linty, so clean your machine more often.
It's a good idea to do some practice runs on a sample sandwich of the actual materials you're going to use to make sure that the thread and tensions play nicely together.