Thanks Diego, that seems to be working. I updated all of the APs to be 802.3at and rebooted a couple of them, while leaving the switch settings at about 17W. The two I rebooted did activate the secondary port and don't seem to be marked as using extra power on the switch.
After hours I'll power-cycle my most loaded switch. It's has 24 POE+ ports, and has 20 R610s attached. If that one comes up normally, then that's definitely the solution.
I guess when I changed the APs to 802.3at previously, I had already messed with the POE settings on those ports that caused them not to be properly powered, or over-powered, depending on the test I was running.
Do you have LLDP turned on on those switch ports?
Thanks!
Dave