Hello jdubin and welcome to the forums! Wish I could answer your question but it sounds very mysterious. Just curious, have you removed the battery and run strictly off the power adapter, moving the laptop, switching between the TP and dock?
If you have and all is well I'd think the power circuits are ok. And if all is ok there, then there'd likely be a battery issue or charging circuit issue.
IBM Thinkpad T41 Home | X31 Travel | X60 fun
2GHz Dothan (X60 C2D, X31 1.7 Banias), 2GB RAM, 320GB HDD, DVD Multi-Burner, IBM 11b/g, Bluetooth II, Docks
multi-boot (98SE, W2K, XP PRO, Win7, Linux Mint 10)