i've had no problems with my flannels, and I back all of my quilts in flannels. I have had to wash the four I have at home LOTS of times and never any pilling or anything. They all came from various LGSs. I would suggest since you are having problems, warm wash and rinse, gentle/handwash cycle with either woolite or the quilters detergent you can get online.
best of luck!