Did you cut all the threads and start from scratch? Serger threads have to be threaded in a specific order. If you are trying to re-thread just a couple of them, they may end up in the wrong order.
My serger has a colored diagram inside the cover with the threads numbered in the order of threading. I loosen all the tension knobs when I re-thread, to make sure the thread gets seated correctly, then re-tighten after threading but before test sewing.
Edit: Oops! Sorry, I think I misread your problem!