I had lots of issues with my BSR when I first got my machine in January (I've never used spray basting). The problem seems to be in the pressure level of the presser foot. The updated spring and washer will help but I have also found a few other things that ensure I don't get skipped stitches.
1) Even though the manual says to put the presser foot pressure level at 0, I put it somewhere in the mid-high 20's, even low 30's if I'm quilting a thin, minimal seam quilt. When the pressure is at 0 the fabric can come up with the needle and "tent" around it, causing the skipped stitches.
2) Use a 90/14 sized needle. Anything less on a regular quilt and I will get skipped stitches. I quilted an applique wall hanging with a smaller needle but there were no seams and the whole sandwhich was very thin.
The only way I can think of that the spray basting is the actual problem is if it's sticking to the needle and causing the "tenting" like I talked about earlier.