Did you ever figure this out? I've tried a single dongle on two separate computers with three different antennas in different locations (inside, outside the window, outside in an open parking lot). It just started occurring a couple days ago when I noticed unitrunker tuning to a channel and then a second later ignoring it when it receives the second duplicate call. Weirdly enough, I've gotten three in a row where Unitrunker tunes to it on the first, ignores when it gets the second, then tunes back on the third. It seems to be happening the most on Dispatch channels and less frequently on the TACs, but I have no idea why it would do that. The control channel is Motorola SmartZone with P25 voice.
When I switched to a different site (P25 control and voice), a user kept having 4-5 duplicates, but it seemed like the other traffic was fine (not nearly as busy of a site as the main one though). This started while I had been running the dongle for much longer than previously (~16 hours), so I'm probably going to pick up another when they restock and see how that goes.
Using a RTL-SDR on both UniTrunker 1.0.32.7 and 1.0.33.5 utilizing both 2 VCOs and 1 VCO (only monitoring control).