I'd try playing PS2 again, now that APM is disabled. See if the same throttling occurs. Prime95 is a 'non ordinary' load scenario, not many programs will apply such a heavy load. I believe that board will run your CPU as stock fine without throttling in normal use. If you were to bench or say do some form of conversion or rendering with the CPU then yeah, it'll throttle.
I'm not sure if there is any other setting on that board which would be throttling the CPU. I had throttling on an M5A97 Pro R 1.0 with a very highly clocked 1090T - and it was due to the VRMs overheating. It just didn't have the quality and quantity of phases to fuel a 4Ghz + core 2900Mhz CPU NB
My board was the M5A97 Pro R 1.0, and had heatsinks on the VRMs unlike the ASUS M5A97 LE R2.0. I'd keep it all stock check its running ok for now, and save for an M5A99FX PRO R2.0 or equivalent to really open the CPU up in the future.
Can we get a screenshot of HWinfo after a AOD and PRime run so we can check it's definitely VRMs and nothing else.