This is truly not always the case. I have just built a new machine using the h100i. This case is a 600t Graphite Corsair (tight fit for it being a corsair case and cooler, the atx power connector needs a bit of finesse) and upon completion of the build I have noticed (doing exactly what the manual says) that prior to installing the OS, the fans work independently except on boot. I am unsure at this time if this is just because the CPU is not under load and the software for the h100i is not installed or configured. I will know more tomorrow. At this point, the machine boots, fans go full speed and then one turns off, then the other one turns on, turning the first one off and vice-versa. I watch this in the bios (temps) for 10 minutes but never got about 35c, basically it say at 34.5 and then flickering to 35c. Even with the fans doing what they were. I will install the OS tomorrow, do all update, tweak and then install the cooler software and see what happens. I will post back if I find anything new. I do believe that once the system is configured that you can remove the USB connector and the cooler will stay as it was set forever. This is a plus since cases like the 600t have 2 USB 2 headers inside and if you are using one for the cooler then the top of the case will only have two functional usb 2 ports temporarily.
Post back when I know more. About 24 hours.
Kind regards,
Saxamo