There are many reasons for the puckering in the back. Starting from the moment you make your sandwich. I tape my back to the floor and then layer the batting and top. I then press the whole sandwich and pin. Start pining in the center of the quilt and work your way out, pressing again if the quilt shifts. When you start to quilt, make sure you use a walking foot. Depending on your machine, it may be very expensive or reasonable. for example, for a Bernina is very expensive, but if your machine is a regular low shank, I found one ay Sears, in the sewing machine section, for under $20.00. If you don't use a walking foot the layers are not fed evenly and that's why they look folded in the back.
I am not sure how your thread get caught on the foot to make the long stitch. It sounds to me more like your machine is skipping stitches, which is due to your needle. Remember that your needle have to go across a much thicker layer and the needle needs to be very sharp. As a rule, I change my needle after every large quilt or after every two small quilts. No need to discard the needle, you can save it for piecing later, when you don't have that many thick layers. Also, if you are using a high loft batting, you may need to increase a little the pressure of the presser foot (if your machine has this function) to make sure the needle can go through all the layers every time. If the needle can not penetrate all the layer, it will not form the stitch and it will look like the stitch was skipped, like when you are sewing jersey.
I hope this helps,
Maria