A couple of things in Planeplotter can give the impression of it tracking flights that don't appear on the Radarbox display:
1. Timeout settings. Try to match your timeout settings between Radarbox and Planeplotter. If your timeout settings in Planeplotter are bigger than those in Radarbox, then obviously aircraft will appear in Planeplotter that have already timed out in Radarbox.
2. The "Predict Postions" setting. If you tick this in Planeplotter, then even after aircraft have timed out in Radarbox, they will continue to move in Planeplotter. This is not REAL movement, but predicted movement in Planeplotter.
During beta testing of port 30003, I tested Planeplotter with identical timeout settings, and "Predict Positions" turned off, and found no discrepancies.