So, after the system has been restarted, the behavior seems mostly the same. Still getting zero minimums for all and a 20k+ RPM max on System 3, but it takes time before those readings occur. And again, a simple restarting of the software returns all values to normal. As for any sort of system behavior that might correlate, I haven't identified any yet. It happens after some random number of hours from starting HWiNFO, the same with HWMonitor.
As for swapping the CPU OPT fan header reading in place of the System 2, that hasn't happened yet, but from the looks of things, given enough time I suspect it will happen again.
Letting HWMonitor run just as long, it had interesting behavior. For whatever reason, despite only 3 of the 5 fan headers on the motherboard being in use, at some point, all 5 were detected as connected and having some measurable RPMs by HWMonitor. Again, I think both piece of software are seeing the values, just reacting differently in how they handle them.
[attachment=3407]
So, Gigabyte advertises smart fan control for all of the fan headers on their current motherboards, including this one, whether you run 3-pin voltage control or 4-pin PWM control fans, and I wonder if there is something peculiar to their fan control, detection, or monitoring that could be contributing to this behavior? I do believe I can manually select the control type in BIOS, so I will see if manual specification has a correlating affect on behavior and report back.