I'm abandoning AI Suite since it can't reliably detect the fans and pumps.
Asus component chat support said:
- PWM Y-splitter cables are not supported on the Maximus VI Gene motherboard fan headers.
- It should work.
After uninstalling and reinstalling AI Suite III with Fan Xpert 2 three times, it's still unable to manage the fans and pumps.
Additionally, the motherboard and AI Suite III appear to be sensitive to the type of PWM chipset used in the fan. CoolJag technical support said they've heard of this type of incompatibility, but there's no fix. However, this isn't the only issue as a 3-pin pump can't be detected either.
Perhaps the Corsair Link Commander Mini or NZXT Grid+ V2 would be more compatible.