If I read you correctly, your Thinkpad had 2 stick of 2GB ram (4GB total), you removed one 2GB stick and added a 4GB stick for a total of 6GB? (and it only recognizes 4GB.)
Check these Thinkpad T400 memory specifications from Lenovo.
https://support.lenovo.com/mx/en/solutions/pd005598
PC3-8500 Non-Parity (NP) Double Data Rate Three (DDR3) Technology
Two SO-DIMM Slots
The use of 1067 MHz SO DIMM memory is recommended for this system.
512 MB, 1 GB, 2GB, or 4GB memory
Supports up to 4GB maximum memory
Note: Only 64-bit operating systems support more than 3GB of system memory (RAM).
So there's your answer; the ThinkPad R400, T400 only supports up to 4GB of RAM... so it was not made to support more than that. You installed the 4GB total in one slot, and it may be recognizing 2GB out of it, you can test the laptop with that 4GB stick alone, and see if it recognizes 2 out of it or the full 4GB.
4GB is be the total RAM a 64 bit Windows will recognize... a 32 bit would recognize only 3GB. The BIOS and CPU-Z only point out that the total installed RAM size is 6GB not that all of it should work.