One thought I have is that the weight of the quilt may be affecting tension intermittently. On a practice piece, you don't have the weight issue. With a real quilt, unless you have a really good setup where the entire quilt is supported all of the time you work, there is a tendency to sew too long before stopping to adjust the quilt. The result is that there will be more weight pulling on some areas of your stitching line than others.
The other idea, assuming you have a bobbin case, is to remove the bobbin case and run a toothpick underneath the spring on the outside of the bobbin case. This is a common area for a small amount of lint to accumulate, and that tiny bit of lint can affect the bobbin thread tension intermittently.