Do you use the same aerials of each of them?
Is it pretty consistent, with one being better on say VHF and the other UHF? Is the difference getting more pronounced?
Back when the BCD396T first came out, I imported one and a good friend, who knows more about radios than me got the UBCD396T (Australian version) and we did some side by side testing. His worked better on 800MHz, where mine was better on the airband. When I got the UBCD396T, we did some more testing and also found some differences between the performance of them.
As a side note, a few years later I ended up buying two of exactly the same radio scanner from a local supplier (these weren't Unidens) however they were literally two serial numbers one after the other.
I programmed both of them exactly the same, exactly the same frequencies, using exactly the same aerial and I found that over time one of them had slightly better performance than the other, to the point that one would open the squelch for a signal, where as the other one wouldn't, so I think that given the cost and production limitations of the scanners that we purchase, it is going to be some differences in performance between different versions of exactly the same model scanner.