Been using APO for a while now... a few months back however I upgraded my PC - including some new overclockable DDR 4 RAM. The base clock speed is 2133, but it can go up to 3200mHz. The program works perfectly (as it did on my old DDR3 PC) at 2133 - 2400 mHz, however when my RAM clockspeed is set anywhere between 2500-3200 mHz I get audible pops every now and again. The faster the clockspeed, the more frequent the pops occur. They seem to be tied to CPU / RAM load, as they won't happen if the PC is idle playing iTunes, etc... but while gaming / scrolling down a webpage such as facebook + listening to music, they happen a ton. The issue ceases the moment I turn off EQ APO. I have even gotten 2 DIFFERENT brands of DDR4 RAM, and it happened on all 3 sets. 2 Sets were 3200 mHz rated, and the 3rd was 3000mHz. No matter what settings I try, it seems once I pass the 2500~ mHz mark the audio just won't stop popping. Really weird issue, as a result I've just been using my RAM at 2300 mHz until a possible fix.
Try exporting your config as a convolution impulse response (use plain dirac as input, use Benchmark.exe -i input_file.wav -o convolved.wav) and use the convolved.wav as "Convolution ..." filter, turn off then everything you did so far (best if you have all your configs in a separate file).