I hope this doesn't sound obvious or padantic or anything of the sort but just to rule everything out, have you tried another computer with the external screen?
Since the normal video output is fine to the internal LCD, It's weird that the laptops VGA ports, the docking stations VGA port and the laptops standard port would both not work in the same way (with the docking station using another port on the bottom of the laptop) both detects the display.
So just to rule it out, I am sure you have already done this but just to be sure, check everything on the external screen before tackling the laptop. It sounds like, based on the question the external monitor might have went to lunch even thou the laptop can sense it's there.
You can also start the laptop with a bootable CD with the laptop fully docked. Something like Knoppix or BartPE, even with something like that something should show up on the external monitor while docked and should rule out anything hardware based if it works.
I can not think of anything else to do right now that could be wrong based on the description of the problem.
Other then calling part of the video card bad and I have not seen a thinkpad do this "exact" problem before, i have worked on quite a few but no expert.