Remove the software you have installed and download Phoebetria. It's better than the official software.
This is the best advice, I tried for an hour or so with the factory software, got it working online etc and even on my iPhone I could manually control it but trying to get the profiles to work was awful.
Download Phoebetria - No need for firefox browser, no silly run as administrator, this thing just works.
After 30 mins of messing about I now have a fully functional, fully automated Fan controller that looks as good as it performs.
A few things to note -
USB header - I have tried a few ways now and it doesn't matter if you plug in the middle part or the end part as long as you have the correct GND/D+/D- wires connecting. There is no 5v due to the Recon getting its power from Molex.
DO NOT USE Bitfenix software - yes you will lose the ability to view over a network when using Phoebetria but if you get the results of a fully automated fan controller then for me its a no brainer
Temp Sensors - Again no rocket science here, if you intend to use the fan controller to be automated then you need to make sure you have at least 1 of these probes attached to a device where the temp changes. I have all 5 of mine hooked up but only 4 fans but you can tell the Phoebetria software which probe to use for what channel, you can use multiple fans for a single probe too.
Profiles - If you prefer not to have the fans spin up to at leats a medium speed when they first turn on then I would suggest setting the fan to never stop. Annoyingly if you don't use this function then when the fan first turns on it does indeed go up to a minimum speed half way or more) before dropping back down to target speed.
Auto Start - My preferred method for this is using task scheduler as you can actually run the program at 'Log In' which can bypass the UAC on Windows 7