Big fan noise problem: the rear fan won't shut off, the BIOS won't update, systemupdate locks up

Question

I received new ThinkStaion (oh boy, lots of memory and CPU speed, yay!)
I unfortunately left the originally installed Vista OS on there.  Very much regretting that as I believe it contributes to the following problems (BIOS).
So the original problem was that after just a month of using my new ThinkStation, the System Board died, and it had to be replaced. Honestly, all I did was choose the sleep or hibernate option in Vista to shut down.  Afterwards,poof! didn't even get the proper Power lights on the system.  I diagnosed this with the online docs and then sat for a few hours on our tech support line doing all the same things to re-diagnose it.  
So after the replacement, the rear fan will not shut off. Jet engine noise all day. I went into the system settings and selected "Quiet" for the Fan settings but that did not help.
Research on this forum resulted in the possibility of a BIOS update fixing the problem.  Comparison to my co-workers systems which arrived at the same time shows this BIOS is woefully out of date, so even if it does not fix the fan issue I want to update it.  However, everything I've tried to do is failing for one reason or another. 
(The fan issue does need resolution since in one week I will end up sharing an office (first time in many years, thanks IBM for nothing!) so since I don't want us both to have to wear noise cancelling headsets, I'd like to fix this without having to just pull the @#$@ power to the fan. Grrrr. )
I downloaded what I felt were the appropriate Lenovo apps to update both the BIOS and the serial number but none seem to work properly from the command line in Vista.  One of the two (can't recall which) asks me to reboot and it never actually shuts down. Eternal "Shutting Down" message. Ga!  The other throws some gosh awful
systemupdate le
http://www-307.ibm.com/pc/support/site.wss/document.do?sitestyle=lenovo&lndocid=MIGR-69701
eternal reboot
BIOSD attempt:" 2xjy26usa
http://www-307.ibm.com/pc/support/site.wss/document.do?sitestyle=lenovo&lndocid=MIGR-69701
error 1275 no admin priv - I AM the administrator account, there is no other acct to use!
Then I decided Vista might be the problem and found sites recommending flashing the BIOS from a bootable USB.  So I started down that path and after burning the wrong version, finally geting the AIK Vista tools installed and to the point of trying to make the USB bootable, it won't allow me to put the OS boot on it.  Ah, for the days when a simple "sys a:" took care of that.
So, after reformatting the USB and pounding my head in the wall, keyboard, etc. I am at my wit's end.  What to do.  I just want the fan noise to go away.
This does seem to duplicate other forum messages but I can't get anywhere on this.  Help!
Solved!
Go to Solution.

Answer 1

FYI to all the helpful folks here (and any looking to shut their jet engine off as well): Flashing the BIOS did the trick.
First I had to find a website with DOS OS files and put those on the USB instead of Vista.  Oldie but a goodie, but at least it booted! No other versions would.
I had been intending to use the WinPhlash utility that Lenovo supplied with the BIOS update but since I was booting from DOS that was useless. However, I found a DOS version of it and used that instead. Boom baby!  Flashed and rebooted. 
It did take two boots to get it back to normal (first one gave very alarming messages about no operating system being found but I think it was just a remnant of the reboot that was triggered from the DOS session).  A second boot returned life to normal and blissful silence from the server.  And I was finally able to get the model and serial number back in there to get rid of the bootup message it throws for that too.
Ahhhhhhh. 
Thanks to all for the hints - I believe I had gotten the idea of flashing the BIOS to solve this from some other thread I found here.  This is a very nice forum to have bookmarked.