I also use the free motion bobbin case (Mine has a blue dot).
I would re-thread my machine from scratch.
I would put my top tension back to normal and try a different thread bobbin on a scrap sandwich and see if you have the same problem. This will tell you if it is truly THAT thread combo that is the problem or if there is a general problem.
Seems odd to me that it would only be one combination of thread.
Watson