Sorry for the delay in posting. I never saw an email about the previous couple posts.
I did not have anything attached to the parallel or serial port. I have some USB devices like my keyboard and mouse and stuff like that.
BTW I tried the bios and it worked fine but I think the only thing it did was to add a single command to disable both ports. The previous bios had the appropriate commands to disable both the serial port and parallel port individually. I bet that would have worked fine now that the issue is understood to be a problem with windows and those 2 external ports.
I tried T60 and T61 and the both worked with the new bios.
Here's a me-too. My T61 was running BIOS v1.26 of 2007-10-18. When docked, losing power to the dock would cause the system to hang. The dock has an external monitor, USB mouse, USB keyboard, and ethernet.
I upgraded to BIOS v2.30 of 2012-04-02. That caused a new option to appear in the BIOS config screen, for the docking station, allowing to enable/disable the legacy ports (parallel and serial). I disabled the ports.
Then after reboot I tested by pulling the power plug and restoring it. The external screen went dark when the dock lost power, but came back immediately after I restored power.
I'm using Ubuntu 13.04 for what that's worth. These hang-on-power-loss-in-dock symptoms don't seem to be tied to the operating system.