It is possible that you put the batting on your frame the first time with the (bumpy) scrim side down
. The scrim is the layer on one side of the batting that sort of holds everything together with glue.
It sounds like you put the scrim side up
on the second quilt and your needle punched the cotton batting through the backing. Most of those dots will probably not show up after the quilt is laundered. Here is some info you might find helpful:http://www.warmcompany.com/wnpage.html
Our newly refined needlepunch technique better distributes the cotton on both sides of the scrim.
You might want to try their Warm Bond: http://www.warmcompany.com/warmbond.html
Warm Bond is the Warm Company's 80/20. Instead of using the non-woven polypropylene scrim that we use in Warm & Natural or glue like other bonded batting use, our poly fiber is manufactured to melt when it is run through a gentle heating process known as calendaring.
I highly recommend that you check out Machine Quilter's Resource for a fabulous source of information and inspiration for long arm quilters:http://mqresource.com/forum/index.php?app=ccs
Like TQS, you need to "join" the web site, but joining is free. However, you will definitely benefit from joining as a Premier member so you can take advantage of the fabulous videos showing lots of long arm techniques!