[XenonSurf]

Your first problem may have to do with harbor raids or when attacking ships very close to a port (around 40-50km).
Because the SH game engine is not designed to attack ships in harbors (IIRC no port ships were included in the stock game for a reason!) it can be that all your traffic gets screwed-up when attacking ships in ports and then leaving the port. That's because all traffic nodes are mostly located around ports.
To avoid this problem, except for the Scapa Flow which has a special script (see GWX manual), avoid attacking ports, also because too easy. If you do, then make a separate savegame to be safe.

For your second problem:
Maybe it's good if you roll back the commander once you are in bunker (port). Something is screwed up in your settings.
The NULL usage is explained in the Commander manual at point 4 on page 31, but it doesn't give much details.