Okay. Pentium 4 Processors are known to throttle when it gets too hot. However, i'm not sure if throttling is done by lowering the FSB.
If it has throttled down because it is too hot, then you should see high temperatures being registered in the BIOS or through a temperature utility. What temperature is your system operating at, have you checked?
Because you've recently done a BIOS upgrade it is most likely that your BIOS is miconfigured. Your FSB should be 166
The first thing i would try doing is resetting your BIOS. Locate the specific jumper on your motherboard to do this, or simply remove the battery for a minute before placing it back again.
If after doing that your FSB is still 99Mhz, and your system is not overheating, then go into your BIOS, locate and correct your FSB speed to 166
To reiterate, your system is currently running at 1243Mhz because your system's FSB has been underclocked or, lowered:
Your processor is currently configured to 12.5 x 99
, which equals the current underclocked speed. The multiplier 12.5 is correct, however the FSB is configured to 99, which is incorrect. It should be configured to 12.5 x 166
effectively giving you a non underclocked or overclocked speed of 2075Mhz.