I've used flannel a couple of times, and have not been disappointed....I washed and dried first (but only once). I, too would only buy from LQS....Joann's just isn't as good.
I've heard you should not use fabric softener with the flannel. It supposedly makes it wear out faster. Perhaps this explains why pajama flannel doesn't seem to hold up. Many of us are in the habit of using the fabric softener products.

Oh! I forgot.....I did have one problem with a wide flannel backing...I bought it from the LQS and there were 2 black stains on it, and they wouldn't wash out. The LQS gave me a replacement piece, but then I found two spots where there was a loose/broken thread. So I had to work around it and put a seam in my backing. I don't recall the brand name, but the LQS owner thought maybe she wouldn't order it again. It was still better quality than anything from Joann's. I would just suggest that you look the fabric over carefully.

Flannel is all I ever use for bed quilts. I like cozy quilts for beds (and so do my grandchildren). I agree with others that it is best to wash and dry it at least twice to make sure it doesn't shrink any more. Enjoy!

I have aquilt on my bed that is over 30 years and its backed with flannel. It still looks good and its very snuggly. Unfortunately I can't say the same for the top.

Be sure to buy the best quality you can afford, and wash and dry a couple times. I love the cuddliness of it, especially for kids and the elderly.

I am getting ready to use flannel for a back on my sons birthday quilt. thank you for all the information. God bless. Penny

I've used good quality unbleached quilter's flannel on both hand and machine quilts. Hand quilting, no issues compared with regular cotton, it quilts beautifully but for machine quilting, be really pernickety with keeping it smoothed out and baste really well. On the scrappy I made my son recently, I did get a wrinkle - ermm, I mean KISS, or two! Other than that, I agree with other posters that it's great, so soft and cosy! My daughter's bed quilt is hand pieced and quilted and backed with flannel and it just gets better with every wash. It's 4 years old an it's washed a LOT!