This is a new build with all new components. System booted fine and I had just installed Windows and the drivers that came with the motherboard. I attempted to update the bios using the MSI Live Update utility from within Windows but this terminated with an error (non specific) and when I rebooted I noticed the CPU fan wasn't working.
I was able to successfully update the bios by flashing from a USB key but the CPU fan still didn't run. I tried tapping the fan and checking for obstructions and also tried to manually set the fan speed in the bios, but this had no effect. I then replaced the Gelid cooler with the stock one and plugged the fan from the Gelid into the SYSFAN2 header in place of the regular case fan and when it booted this time there was a snap crackle and pop followed by about an inch of orange flame from the motherboard. The fan on the stock heat sink didn't run either.
This is the damage towards the bottom left corner of the socket:
I took the fan out and rebooted and surprisingly it posted and booted into Windows despite the damage. At that point I thought I should leave it before I fried anything else.
Does anyone have any idea on what could have caused this?
I've focused on the fan because that's what I was moving around and the damage was near the fan header, but how likely is it that a faulty fan could cause that kind of short in the board? I've had a look at the fans and there are no bare wires or signs of damage on them.
I've checked the case and all the standoffs are placed correctly and I couldn't see any sign of a short but could it have been the i/o shield?
I had a USB keyboard and mouse plugged in, as well as a USB stick, all in the rear panel. The case front panel connections were all hooked up as well as an optical drive, SSD and HDD.
I'll replace the motherboard and stick to the stock heat sink for now but I'm concerned that the problem could be elsewhere and I don't want to fry another board or damage the CPU etc.
I'm pretty sure it was just a short on the board. A weak printed circuit can have that effect. Have you started the RMA Process yet? If so and they've already agreed to take it back for repair or replacement the next thing I would do is reconnect the Gelid Tranquillo Rev 2 heatsink/fan just to make sure the motherboard didn't damage it any. Then, if there is nothing wrong with it you should be able to use it on the new board. Just plugging it in to any other fan header should do the trick. You don't have to actually replace the heatsink to check it. I seriously doubt that ANY fan could cause or effect damage like a motherboard shooting flames, and that's all it is - just a fan. Now, if it was a tec cooler or something like that I might could see it causing some serious thing like that, but not just a fan.