Makes little difference what level of usage a system is or isn't at. If it is still on the air with an active control channel it should be in the DB. You know as well as I do that just because a base gets a 380 site, that it doesn't mean their old VHF system just vanishes into thin air. (Saufley Field ring a bell?)
grossmanms - After trying the freqs. Dan posted please report if any are still an active control channel. If so then this system needs to be put in the DB, regardless of it's level of usage or lack thereof.
As to your intial inquiry any number of things could be giving you problems.
Do you have more than just the primary CC loaded?
Most software programs have a setting to download just primary CC's, primary +alt CC's, or all freqs. (more on why this matters below)
Can you hold on the system then find the active control channel by selecting each programmed freq.?
Even at 5 miles with the stock antenna you may not be receiving a strong enough signal for proper decoding. Many of these sites are notoriously only powerful enough to cover just their intended area plus very little more and stock scanner antennas are notoriously bad at picking up most anything other than the strongest of signals.
Are you seeing any info displayed while holding on the active control channel if you can indeed hear it?
For the time being be sure you have all listed freqs. for the site programmed. Most of these sites are known to rotate control channels regularly and it is possible there has also been a change to this rotation. At the very least you will most certainly need to have both the primary and alt CC's loaded.
The groups that are posted may have all gone encrypted.
Set the system to ID SEARCH mode to possibly discover any unknown TGIDs.
As metioned is the system type set to P25 Standard?
Make sure you haven't inadvertently turned on attenuation.
Please be sure to report anything you find that may have changed or is missing.