Boat won't get over 3500RPM

I have a 2000 Supra Launch with a 325 Indmar assault. Motor runs great until I slam it with sacs. Around 2.5k of ballast and the motor will not go over 3500RPM with the throttle to the floor. So I turn the boat off and kill the master power switch to cut all the juice from the batteries. Start the boat back up minus a 250# sac and she runs like a champ. I dont get it? Even if I needed to reprop the motor is still going into a "protection" mode. Any ideas? I had all the filters and fluids changed about 30 hrs ago so I should be good on that.