An odd problem (For me it is)

Hi guys and girls, I've got an odd problem and am unsure as to how I should progress it.

Basically I've added an Arctic Cooling system to my CPU because the original cooler was a bit on the noisy side, having read many product reviews I picked the Freezer Pro 7 Rev 2. It's fitted and a point.
When the fan is plugged into the CPU fan header I get a weird beep sequence and my system fails to start, so as an experiment I plugged the new fan into my fan controller and only connected the original fan electrically, thus powering both, I've got a temp sensor for the controller anchored at the Freezer Pro 7's base as close to the CPU as possible so I can run the fan on auto. In this configuration I get no beeps and everything runs as normal. I did notice when the Freezer Pro arrived that it's connector was wired differently to the original so looking at the connector with the lugs uppermost (as it plugs onto the header) it's wired Black, Red, Blue and Yellow reading from left to right, the Blue and Yellow were originally the other way around but figured that it was assembled wrong so swapped then about to match the original cooler fan connector.

I've looked up the beep code I get but again it's not really clear what's wrong, it's basically a double beep, pause, then 4 beeps but only when the Freezer Pro fan is plugged into the mobo header, other than the swap of the Freezer Pro plug pins I've done little apart from run it with the above set up and I'm a little puzzled???, it looks like the Freezer Pro fan is causing it but the fan runs with no issues when connected to either the mobo or fan controller headers, I'd rather not have to buy a new cooler before at least asking for anyone's thoughts or suggestions.

I'm running my system at factory settings so no overclocking done (yet), I do know the BIOS is 4 years out of date but the info I have suggests I don't need to update it. I do know my system isn't overheating but I had planned on over clocking it in the future, this little snag has put that plan on hold for the time being. I don't really stress my system, just play games and such but this bug is annoying me.

System details

MOBO - ASUS m4a88t V evo/USB 3
CPU - AMD Phenom II X6 1090T
Graphics Card - Nvidia GeForce GTX 550 Ti
Memory - 8GB Kingston DDR3 1333
Main HDD - WD 500GB 7200rpm 3.5" SATA
Secondary - WD Caviar Black 1TB HDD 7200rpm SATA
Back up drive - Seagate ST350041 8AS 500 GB USB
CD/DVD - Optiarc AD-5280S SATA
Fan Controller - NZXT Sentry 2 Touch Screen (in middle 5.25 bay)
Case - Cooler Master HAF X Full Tower
PSU - Corsair TX850

I've got a couple of extra USB cards but taking them out made no difference to the problem

External Peripherals
Razer DeathAdder 2013 usb mouse (not wireless)
Deskjet D1560 printer
Toshiba Regza 37" TV (monitor)
Crappy 3rd party USB webcam
Bamboo graphics Tablet and pen (USB)
TP-LINK USB Wireless modem
Creative headset (can't find model number)
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Okay, a quick update. I think I've fixed the Freezer Pro problem, seems in my desire to get it working I made a mistake in changing the way it's mobo connector was wired. I returned it to the original wiring configuration, plugged it into the header and hey beeps and it's up and running, no more's currently running at about 1400 rpm, nice and quiet, CPU temp is about 43 degrees C, updated the BIOS to it's latest version while I was at it. So far it's been ticking over at about that speed for a few hours now so I reckon it's fixed.

Thanks to all those who had a look at my fault, next time I'll be a bit more patient and try not to make such a basic error

Cheers everyone