If both sides are doing it, it sounds like a bad SET of ballasts. In my experience when one ballast is bad the other has a 90% chance of being bad also. When power is the issue, ballasts will generally "Mis-Fire" quite often and not so much occasionally. A bad BULB is also a possibility, contrary to popular belief; its not always the ballast that are DOA. But with the harness installed, I can guarentee power is not the issue here!
As long as you have a good connection to the positive battery terminal, and have good bare metal grounds to the two eyelets to the immediate right and left of the relay bank; your golden. Every harness that I build is tested before it is shipped out, so the harness is not the issue.
What I would recommend doing is to test the ballast by swapping the bulb from the ballast that's giving you issues to the one that is not. This will help you to tell you if its the bulb or ballast. If you swap the bulb to a known good ballast, and it still give you an issue; its the bulb. IF it doesn't, then the ballast is the issue most likely. Fell free to give me a call, and I'll be more then happy to help you additionally to diagnose the issue your having with the HID's. I'm here to help Dustin!