One more thing about your monofilament. What brand are you using? And how are you feeding it to your machine? Nowadays when I use monofilament for machine applique, I use my Superior Thread stand (along with a thread net) to provide very nice, even thread flow without resistance to my machine. Here's a link to the thread stand I love:
http://www.superiorthreads.com/shop/...thread-holder/
However, from your description of the issue, it seems much more likely that your bobbin thread needs more tension on it.