Hypothesis: Plunder is mathematically determined by several equations. Used to be 4 or 5 but with highlands I believe this number has increased. The equation used is based on your strength relative to the target strength. As you get more powerful you move into different "plunder equations" vs the same OSF. This change of equation is usually is not noticed. However, It is possible that you have hit an upgrade that had a plunder increase not quite high enough to compensate for the equation change. You will likely see a larger than normal jump with your next upgrade. /Hypothesis
I had max ally plunder go down upgrading to a lvl three Titan. Same scenario as orig poster. I had the same thing happen upgrading a SOS from level two to three. I'm a mixed build. I record test my ally plunder after every upgrade.