Did you ever find the exact problem? I have seen dirt in the piston area cause velocity fluctuations before. The regulator is also one of the more likely culprits, especially when they get old and hardened, and get disturbed when the valve is taken apart. The bottle regulator can cause minor issues, but is less likely to be the culprit due to the big swing in pressure that would be required in order to cause enough of a difference in the mag regulator. A bottle regulator is more likely to have flow issues causing drop off during rapid fire situations than fluctuations in velocity. Another major source of velocity fluctuations is bad paint. This can be more exaggerated with some barrels than with others depending on the paint to barrel mismatch.
Except for the Automag in front, its usually the man behind the equipment that counts.