I also have a S1200BTL motherboard with a E31260L Xeon CPU, and a P4303xxsfcnna chassis . And I've experienced the same problems as described above. But I've been able to locate the problem to a dependancy of ambient air temperature.
Initially I had a an Arctic Freezer 7 PRO Rev 2(http://www.arctic.ac/eu_en/freezer-7-64-pro.html). The server is located next to a door that leads directly out which means that if I open the door then air with outdoor temperature is fed into the server. So what happened (in May last year) was that I noticed that if I opened the door when it was around 10C outside and let the door stay open for a few minutes then the chassie fan started to run at 6000rpm making the server sound like a jetplane with the amber led flashing on the front panel. I could then see in the sysinfo logs that the CPU fan was running too slow and obviously getting under some threshold limit. It seems like the CPU cooler is so efficient that when ambient temperature goes down below room-temperature then the fan provides enough cooling even if running below the fan speed threshold programmed into BIOS. So what happens is that some supervision function sees that the CPU fan speed is too low and puts in into some emergency mode which means that CPU fan runs at 1900rpm and the chassie fan at 5900rpm. And the only way to reset this mode is to completely shut down the server and unplug the power cord.
Note that the S1200BT TPS (Technical Product Specification) states that the board Operating Temperature is 0C to 55C, and in my case has the temperature never been below 0C. Not even close. I even had to put a 2kW fan in front of the server while it was running at room temperature to prohibit it from putting the fans into panic mode.
I've had a support case with Intel Server support since May last year, and I've changed the motherboard, chassie, 2 fans (Arctic + Intel) but still the same problem. And it has been really frustrating to have to deal with those guys because their main effort has all the time been to explain why they shouldn't have to do anything. The last they did before closing the case without asking me was to say that "it was expected behavior" what I had described for them.
Bottom line is: Intel product support sucks! When they are given a real problem then they are unable to handle it, to seriously analyze it and provide a solution making the product conform to the TPS.
I would recommend everyone who face the same kind of problem: Contact Intel and make them aware of the problem. If enough people show that this is a real problem then perhaps someone at a higher management level realizes that something has to be done.
And not buy an Intel server ever again.