Lol, ok, I'm an idiot. I was wracking my brain thinking of anything that could be the problem. The fan still hasn't been ramping up and down via the PWM signal according to the temp sensor on the heatsink. I have a DS18B20 sensor that looks like a BC549 transistor, sunk into my heatsink with thermal compound and that's controlling my fans. I also have another one that is attached to a cable and sealed in an encased water proof housing like in your manual.
So I wondered if it was working properly. As soon as I grabbed it and watched the temp on the monitor go up, I realized the fan was speeding up
Duh, I must have either screwed up the pin assignments or something. It's been a long while since I set this all up, so I have to go back and read in the manual what's making all this work.
But at least I've got an idea what's wrong now! LOL
I haven't fixed it yet, but I'm still relieved.