According to the README.TXT file that was in the ZIP with the BIOS's the X#_1959.bin is for v1.0 - v1.5 the X3_1959_v16Plus.bin is for v1.6/v1.6b versions.
Here is a paste from the README.TXT
<snip>
X3 Config Live Build 1959
If you discover any bugs or wish to post successful test results please use this forum.
http://www.teamxecuter.com/index.php?name=Forums&file=viewtopic&t=23008
The v1.6plus version of this bios is now compatible with v1.6b Both versions have
been tested and fully working on all versions / regions of Xbox.
Make sure you follow the diagrams and instructions to the letter - or you WILL have problems.
The default.xbe (x3_erase) app is to erase all settings from the X3 EEprom in case you forget your password
and lock yourself out of X3 Config Live. This does NOT reset your video settings as they are stored on your
Xbox EEprom and not the X3.
X3_1959.bin is for v1.0 - v1.5 Xbox Versions
X3_1959_v16plus.bin is for v1.6/v1.6b Xbox Versions.
For v1.6b detection RAM is usually Hynix and v1.6 RAM is usually Samsung
For Support help and advice please visit
www.teamxecuter.com
</snip>