This happens when the 'new' ai flightplans are an edit of the default flightplans. Typically the author will simply substitute ai aircraft with 'real world' liveries for the default ai aircraft (usually airlines) and recompile the flightplans with a new name.
As 2004 can have multiple flightplans (traffic_*.bgl files), you end up with multiple instances of the generic ga and commercial flights.
A few ways too remedy this:
Edit the duplicate flights out of the flightplans using TTools, a daunting task.
Use only one of the flightplans at any time by moving the others (out of the sim), or renaming the other 'traffic_*.bgl' files (something like 'traffic_*.bbb).
Stick to add-on flightplans as you would get from AI web sites, such as ProjectAI. These are normally 'custom' built and do not include any part of the default flightplans.
Dave
At that time [1909] the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation. Igor Sikorsky
I intend to live forever....so far, so good. Steven Wright
You know....you can just rip up a to-do list.