Yeah, the character is standing on a dark BAKED shadow.
I don't think it should be correct to read the texture color in this case. A dark or light floor doesn't necessarily mean a light or a shadow.
Unless I take the next c_trace, making sure it's a block and not arbitrary geometry (can this be done?). But even if it's possible, I'd have to reproduce the lights using blocks in WED.
I have heard of a second set of uv coordinates in MED, and soon in the engine. I wonder what can be done with them.
EDIT: I should have read the beta log more carefully:
(X) MEDB now supports a second UV set on skins, for special purposes such as shadow mapping. The second UV set is also stored in the MDL7 file, but not yet used by the engine.
I assume a solution is underway.