Latest version is Version 1.04.00. but changes have nothing to do with rebanding options, Adds some features like motorola sub id's or better known as unit id's . Your firmware is ok as far as tracking newly rebanded systems.
The bcd996xt has the ability to track rebanded motorola type II but has to be set up like everything else. It is available in firmware. But you have to set it up to match the system you are monitoring.
The first thing you need to do is download FreeScan and get a connection to your computer. Use rs232 cables provided via the front panel of your radio.
Once you have a connection between your scanner and freescan software spend sometime learning how to use it. Then you can get a premium subsription to Radio Reference and download the trunking and conventional systems to freescan then upload them to your radio. Rebanding issues are taken care of by radio reference.
If you are not used to dynamic memory type scanners you will have a steep learning curve. Ask alot of questions in this forum.