I have a 6600 and when I started practicing FMQ I never seemed to get good stitches and could never get the top and bottom balanced so just used the same colors in both. The stitches didn't much improve and I thought I just needed more practice. I was using the blue dot bobbin case and washers. One time I started FMQing and forgot to change out the bobbin case and had the most beautiful stitches ever! I was amazed. I also was using Superior So Fine in top and bobbin and didn't drop the feed dogs and was using a 80/12 top stitch needle. It seemed like the perfect recipe. Then I read on the 6500 yahoo group that someone had purchased the straight stitch needle plate and had really good results - so I purchased it and now I can use almost any kind of thread. I still use an 80 top stitch needle, don't drop the feed dogs and use the red bobbin case. Sadly I still get dots on top if I use different colors so I just use the same colors or very similar. I'm just happy to get great stitches.
Sorry to hear about your frustration. Please keep us posted as to how it all works out.
Hugs, Kim