Well. I hate to break it to you, but sometimes you just can't fix it. There is a quilt shop owner in my area who quilts professionally. She has two top-of-the-line Gammills in her shop, and she always uses the same thread top and bottom because it disguises the "pokies". Sometimes even the expensive machines, run by experienced quilters, do this.
Sometimes it's easier to pick a busy backing fabric that the thread disappears into. Or, realize that your quilting design will be visible on the back, but since no one ever looks at the back, who cares? (unless you plan on showing it).