Totally understand and Hopefully we can get your faith in is back. We will try and sort it out as quick as possible for you. Due to the age warranty will be the only problem but we will figure all that out with you and we will discuss the options.
I can think of a couple of reasons why you would NOT connect that fan header to the motherboard:
1. Motherboard might not be able to supply the required power to the pump. Amps on motherboard fan headers can be too low for pumps.
2. Motherboard might try and regulate the speed of the "fan" not realising it's actually connected to a water pump. The water loop probably has it's own settings for speed, or has one set speed.
Even if your pump had failed, the CPU would have overheated and it's protection would have kicked in to stop it being fried.
So the shop has got the basics wrong.
Glad you wrote this as I'm in the middle of setting up a system with water cooling and it had completely skipped my mind to consider what the fan connection was plugged into.
Their diagnosis is completely wrong! You WANT the pump connected to a constant power source such as the PSU and the fan on the radiator to be connected to the CPU_FAN header, otherwise the speed of the pump may be varied based on the CPU temperature which you do not want, you want the pump to always run at a constant speed!
Thought I would just clarify a few things as an ex OcUK builder.
The reason we plug the Pump in to the molex to fan cable (that female 3 pin to male 4 pin) is actually to protect to board, the pump draws more amps than a standard fan, more than most boards can handle, having this draw going through your motherboard can cause it to burn out. Plugging the pump in to the board therefore actually has a higher risk of damaging board. (which I notice a few people have also said)
Some systems might have separate cables for monitoring and power, or maybe for the radiator fan. You pretty much always power the pump itself from the PSU rather than the motherboard headers. Self-contained systems often just plug straight into the PSU and run everything else off that connection.
Gj OCUK
Dont forget we all wanna know what you find at fault aswell
A quick update:
We are getting this guys system back out of warranty, just as a gesture of good will, any components in warranty on the order we will replace where needed, any not in warranty we are giving him the option of ordering replacements from us and we will fit the parts he orders to replace the faulty parts.
Basically because of his hassle with "Silicon" we are doing a free diagnosis for him, but I will stress this is not something commonly done, we are also curious as to the extent of what has occurred and to ensure that nothing has been done wrong at our end initially, though we are fairly confident of this, we would like to double check.
If your system is out of warranty (We now offer 2 years as standard since November 2012, please ask us if you are unsure as it may not apply to all systems) while we will offer support via our forums unfortunately diagnosis we ask that you either do yourselves or get done by a professional.
Proper diagnosis involves replacing parts until the system works again, if a computer company just looks at a computer and goes "That's your problem there" I personally would advise to never deal with that company again, because unless you personally have changed something, the system wouldn't have failed over something visual after a years use (excluding occurrences such as leaking fluid, but even then diagnosis should be done by checking all the components as it may have affected other parts)
Any faulty parts within individual warranty we will also send off to be repaired or replaced where possible (partial refunds relative to current value may be given if no repair or replacement is available)
Just contact the RMA team for faulty parts here:
https://www.overclockers.co.uk/webnote.php#rma
Hope this helps