I have had my 8900 for two years, and I've never had an issue with the timing after sewing multiple layers. I make a lot of bags, and sometimes that involves sewing eight layers of quilting cotton plus two layers of fusible fleece, or more. I do sew slowly when I have that many layers.
If you're on Facebook, you may want to reach out to Janome there. Another dealer or user may have a suggestion for you based on a similar experience or Janome may respond to the "squeaky wheel".
Have you checked the warranty you got to see if it explicitly excludes timing issues? I have no idea how the dealer would determine it is "operator error" that caused the timing to go out the second time. Sewing four layers of cotton wouldn't do it unless there's something else you're doing.