Hadi asked me about this behavior that I suppose isn't really a bug so much as an accessibility oversight. We were able to work through it, though since it's easier to explain with pictures, I took the liberty of writing the report.
Reproduction steps
1. Launch Aurora 1.6.3
2. Open the Federated Nations game.
3. Open the Naval Organization window.
4. Using the mouse, select SRV Federation Survey Command (CAPT) - Home World. Make sure it is expanded.
5. Using the keyboard this time, press the down arrow to select the GEV Ferdinand Magellan fleet. This is where the problem appears.
Once you select that fleet, the focus moves over to this location with the red box around it, meaning that further keyboard navigation doesn't apply to the list of fleets on the left.

Hadi has expressed that this is undesired behavior, as that may not be the fleet they were going for. This is only a problem if you use the keyboard to navigate, though.
Since I obviously can't read your source code, I don't know how easy this would be to do, but my first guess for a solution would be to call the
Control.Focus method to refocus the list on the left side of the Naval Org window as the last step of whatever happens when you select that fleet. It doesn't matter to anyone using the mouse what's in focus, as they'll just click on whatever it is that they need to click.