I don't know if the P25 Threshold settings get carried over when programmed from a file. They were hidden settings at one point but I vaguely recall them being made always visible during a firmware update a while back.
They are under the settings menu.
The only other thing was some hardware changes during 2020/2021 for many of the Uniden scanners. I can't find FCC documents for the 996P2 but the 325P2 is this:
I have no idea if this kind of component swap would make the kind of differences you are experiencing.