I also use Superior Titanium Topstitch needles in my Juki TL98Q (older model than yours but basically the same machine). I LOVE those needles and use various sizes for every kind of thread, cotton, poly, rayon, silk, metallic, and they work GREAT. I get them at my LQS, but you can also order them directly from Superior Threads online.

It may not be a needle issue as much as it is a thread issue ! Variegated thread is not all the same weight, it may be off just a very small amount, but it does change from color to color due to different dyes being used to produce different shades / colors ! My suggestion would be to run a test sandwich through with the variegated thread and then again with a solid color thread and see if you notice a difference.