I can't say for sure what the problem is, but here are the steps I review whenever I have an issue with stitches not forming properly on the bottom:
1) Put in a new needle (should be changed every 8 hours, anyways). Needle should be the recommended size & type that your thread manufacturer recommends (for Aurifil 50/2 thread, I use a #80 quilting needle)
2) Re-thread the top & the bottom according to machine instructions. Be sure to cut thread by spool & pull from by needle. It will pull out any fuzzies that way ... usually.
3) Make sure top & bottom thread are the same unless using monofiliment in the top.
4) Put together a 12x12" quilt sandwich with your scraps & play around with the TOP tension. Probably need to tighten the top tension by 0.5-1 level.
I don't know how many FMQ projects you've done to date. If this is your first, get yourself a yard or two of JAF/HL/Wal-Mart clearance bin fabric. Cut it in half & put whatever batting you normally use in the center. Then spend a few hours practicing. If I really had to guess, I'd guess you're not moving the fabric fast enough through the machine. One thing that's helped me a lot besides practicing has been to draw quilting lines on the fabric. I like using the Crayola Ultra-Clean markers or crayons because I can get a lot of colors that show up well, but you can do it with chalk or the Blue Water Soluble or Frixion pens, too. It's one less thing to distract you from focusing on your speed when doing FMQ. In addition, lighter weight threads tend to be a bit easier to work with than heavier weight threads. So if you're still struggling, cut yourself a break & pick a nice lightweight variegated thread (50/2 aurifil cotton or even a 100wt YLI silk) that matches the background of your quilt.
Best wishes with your project! I love that you did a pieced back!