You did connect the USB cable from the pump to the MoBo, right? Look your H100i GTX manual, page 6.
Without that USB cable, there's no way Corsair Link can detect your AIO, which enables you to control the pump and rad fans RPM.
Yes, I tried both of my USB 2.0 headers to no avail. They both work though because I tested out my case USB 2.0 ports on both headers.!