There's a setting in the TPFanControl.ini (which you can edit) which sets the fan speed mode back to Fan128 at around 90 C, which is BIOS. It seems that by default Thinkpads don't like to spin their fans up, so this is actually counterproductive.
TPFanControl says:
// Fan speed of 64 is extreme and may be an *unsupported*
// and *damaging* mode. A fan speed of 128 setting is
// not really a fan speed in itself but will instead switch
// fan control to BIOS mode (0x80). The idea of this
// is to let the program get out of the way and let the
// BIOS handle extremes.(and then switch back to smart if
// the temperature is okay again)
I guess most people use TPFanControl to make their fans quieter. Other people like me use it to make the fan spin faster.
Near the end of TPFanControl.ini there are the speed and level controls for Smart Mode 1 and 2. It looks like this:
Level=(Celcius) (Fan Speed Mode)
eg.
Level=50 0 (fan off)
Level=55 1
Level=65 3
Level=75 7
Level=80 64
Level=90 128 <-- Replace 128 with 64 or // off this attribute.
This has been my experience with TPFanControl.

I've used it on IBM T42p and R50p and Lenovo T500. I've found that the IBM fans are much more responsive, they report temperatures faster and change speeds faster than the T500's fan. It could just be my computer tho, but you can watch how drastic the reported temperatures change (ones to look out for are typically CPU and GPU) and if they're rising too fast the fan may not speed up fast enough to cool the computer down, in which case you'd want to set the fan to run faster at lower temperatures to preempt this. I think this should only be a problem on high wattage CPUs like 35 watt Intel T CPUs.