My T21 (2647-47U) has been running BIOS version 1.16 (KZET34WW) 2004-04-28 and imbedded controller version 1.06 for several years and I have not experienced an over-heating problem. I've even upgraded to a 1GHz CPU with a T22 fan/heatsink and its not overheated.
I think your problem is something else.
Have you checked your CPU temp with MobileMeter? This little utility will read your CPU and HDD temp. I have it installed on my T21 and occasionally check my temps.
You can download it here:
http://www.softpedia.com/get/System/Sys ... eter.shtml
EDIT: With the CPU idling, the original 800MHz CPU would run at around 41°C and the fan was not running. Under high CPU utilitation, the fan came on at around 79°C and immediately started dropping the temp to around 70°C and held it there until the CPU utilization dropped.
The 1GHz CPU runs just about the same except its idle temp is around 44°C and the fan is not running.
My 7200RPM HDD's temp is usually around 41°C.
All of these readings were taken with no PCMCIA cards installed because those slots are very close to the CPU and generate a lot of their own heat.