Does the back of the rear end cap butt up against the barrel in back of the threads? If it doesn't then this is the likely cause of the misalignment. Threads are only supposed to hold the thing on, not properly align it.
Here is a thread guide. http://www.silencertalk.com/AAC-thread-guide.pdf
Some look like yours, others have a relief groove. I think a relief groove is going to solve your problems. I would go with whatever advice the silencer maker gives.