It could be that the scanners reference frequency are too much off from it's nominal value. It then will have more problem to decode a digital signal if it is more distorted. It's a bit difficult to test without a signal generator but a telltale sign could be if a FM setting instead of a correct NFM will improve reception, if the transmission are actually done in NFM.
/Ubbe
I had this exact thing happen on one of my states new VHF sites not long after the system went live in my part of the state.
The VHF sites here are all single tower non-simulcast sites. The site in question worked fine in NFM mode for a couple months after the system went live. Then one day I noticed no reception from one site. The nice signal level was still there but no decode of the CC.
I found I could still decode the sites control channel just fine with a GRE model but nothing on my x36HP models. The same x36HP models received the CC just fine from the other VHF sites within range. That pointed to an issue with the site.
I first changed the bandplan setting using Sentinel so the troubled site would use FM instead of NFM. That worked and the x36 was again decoding the bad sites CC just fine. The other sites using the same frequency range were also now using the bandplans FM setting but they still decoded fine.
After this worked for a week or two, I finally did a manual edit of the favorite list for that system and changed the mode to FM for just the one site with the problem so I could put the bandplan back to normal for the other sites. I needed that trick in place for another month or two before the problem was fixed at the transmit site.
I was able to put that site back to auto mode and all's been happy since. This was a couple or more years ago since that happened.