Is it receiving a signal on those frequencies and not decoding? Did it stop decoding after you dated the firmware? I had that issue with my Pro-96 and LAPD APCO-25 transmissions many years ago. I upgraded and all of a sudden the digital signal would drop out and all I'd hear was noise. I downgraded to the former firmware and it has been fine.
It could also be, as KA3JJZ pointed out, that the radios are out of alignment. I'd say that is less likely if you can correlate the problem to the firmware upgrade. Anyway, if it is an alignment issue, Google "Pro-96 VR4 alignment" and you should find some RR posts about that. VR4 seems to have something to do with 800 Mhz alignment, so if these are UHF digital signals, adjusting VR4 will not work. Maybe I'm lucky, but I've had my Pro96 for almost 20 years now and it is still spot on.