For me, polyester thread and batiks do not get along together, I've always matched my thread with what my fabric is. Since batiks are cotton, I only use cotton thread. I can't remember what size needle I'm using currently, but Aurifil has some fantastic cotton thread, 30 weight that I'm using for my grandmother's flower garden.
You might also consider re-threading a new bobbin and pay attention to how it's being threaded. I actually just went through this not too long ago, there's a video on YouTube that shows how a bobbin should be threaded correctly and it fixed my skipped stitches. I was surprised to discover that something as simple as threading a bobbin can cause issues if you don't do it the right way. I did change out my needle, as well.