Hello there, my name is ***** ***** I will be working with you on this issue. Everything I have read about the T41 with a flashing ***** *****ght indicates a bad battery. Although there may be a voltage across 3 batteries, but that isn't the whole circuit. You indicated that there were 6 batteries. Can you measure the voltage on the output pins of the actual battery housing? It is possible that the protection circuitry in the battery has been blown while opening the battery housing, removing old batteries and reconnecting the circuit when installing the 2 new batteries.
Do you have another battery for this laptop that you can verify will charge in it still? Also, you wouldn't happen to have access to another T41 (or other Lenovo Laptop which uses this battery) in which you could place this battery in and see if the behavior moves with the battery, or stays with the laptop.
If you want to try to reset everything, you could try removing the battery, unplugging the power adapter, then pressing and holding the power button on the Laptop for 30 seconds or so. Then put the battery back in, plug in the power supply and see if the problem goes away.
Another possibility is that the power adapter isn't the correct adapter for this laptop. I have seen cases where, even though the power adapter is the correct voltage and current and the plug fits into the laptop, if it doesn't have the correct chip to identify it to the laptop, the laptop will not charge. It will still run on the power adapter, but it will not allow the battery to charge. Are you using the original OEM power adapter that came with the laptop?