Jason,
In Preferences/Radarbox, what setting do you have for Filter garbled Flight ID,s and Squwaks. If its ticked untick it to see how it goes and if its unticked , tick it.
Unfortunately mode-s aircraft cannot be error checked the same as ADSB aircraft. We have it set to be the same message received on 2 consecutive signals, any more and flights are not displayed as they would be filtered out because we could not confirm the correct aircraft. We had it set to 5 at first which was very good but too many flight were not displayed especially in areas of poor radar coverage. Two was the best compromise between display and not display even if a few error crept in in the flight ID's. Other boxes had the same problem and they went for 2 as well.
Alan