So, I've done more testing. I think this is maybe a BIOS problem. For the record, I'm running version 0701 on my board. Under normal circumstances the voltages are as I posted in my first post. However the wrinkle comes in when I tried fan xpert2. When using any of the preset "Profiles", i.e. Silent, Standard, or Turbo, the voltage is still 2-3v lower than the other headers. But, if I click the "Full Speed" button at the bottom of fan xpert2 the fans spin up correctly and ALL the headers read 11.99v on my multimeter, includes chassis_fan1. What's up with that? Presumably, based on this information. the header is functioning normally and CAN provide 12v to the fan. The question is why doesn't it do that normally like the other headers?
If someone else with a Gene V could check their board that would be most helpful.