Do a little test yourself. Swap the "good" A2 head for the "bad" one. Now see if there is a corresponding difference in the LED's. Then, if you're skillful, and using JS advice on how to take the LED ring out very carefully, swap LED rings in both heads, and check for a difference. By now you will know if the regulator in the body is causing the LED's to flash brighter, or if the LED rings are different.
Also, try taking the MA02 lamp out of the head in both lights. Now screw the head back on. Turn the tailcap switch to the LED only position, then, slowly continue to screw the tailcap to full on. You should see a minimal change of intensity on the LED's at this point, as the 10 ohm resistor in the tailcap is bypassed and the LED's go into direct drive. I doubt however that this minimal difference matched your claimed marked difference, or I would argue that your tailcap is defective. You see, your LED's, even in direct drive configuration, should not be that bright. Unless they are different LED's, which might be the case.
Some good reading for you
https://www.candlepowerforums.com/threads/107943
On a side note, I am skeptical on your observations. I own a very bright green A2, as well as all other colors. The super bright green A2 could never match my Kroma' beautiful, uniform, and bright red beam on high. At least if you are comparing it to a regular 8 red LED Kroma, as opposed to the 4 red LED Milspec Kroma.