This issue is occuring for me since a very long time; using Windows the fans have a much higher speed setting compared to using Linux and the thinkpad-acpi driver. However, since the use of Maverick I experience a lot more automatic shutdowns, triggered by thinkpad-acpi, due to overheating. Before, I was using Karmic and also experienced it sometimes.
When monitoring the temperatures manually and setting a fan speed accordingly the CPU is cooled properly, but thinkpad-acpi never triggers higher CPU fan speeds even when > 95 °C! That is, in my opinion, a bug.
I'm having this issue on my T61p - C2D T9300 w/ Nvidia QuadroFX 570M. Both need quite a lot of cooling, especially when using the docking station (less ventilation, more isolation on the bottom).
That's why I don't think this issue is specific for one Thinkpad model, but occuring as soon as you start using thinkpad-acpi, also in older versions of Ubuntu. And yes, it's a universe piece of software not part of the core of Ubuntu, but this should really be fixed as it might cause hardware failures.
I think running a user space software daemon as a workaround is rather 'dirty'.
More hardware related, but still not justifying the behaviour of thinkpad-acpi:
I noticed there was an awful lot of thermal grease on both the CPU and the GPU for the integrated heatsink/fan in my Thinkpad, I cleaned it, replaced this with a proper amount of thermal grease and temperatures are 10 °C lower since then.