Oh, I can take a look at that if you'd like - it was my code originally, I might as well dig in and fix it.
That said, it may also be worth taking another look at what, exactly, siege mode -does-. When I first implemented it, my idea was that it was designed to primarily give a boost to energy weapons, to encourage using them over ballistics. As the ships that use it no longer have the option of mounting ballistic weapons, that entire notion is a bit obsolete.
In fact, I might even suggest turning it around entirely; the AI doesn't really know what to do with a ship system that slows it down, but if you made the hulls normally slow, then a "pursuit mode" system that diverted power from other systems to engines might be easier to get the AI to make proper use of?
...On the other hand, ships with mobility systems are pretty common; doing something different is definitely worth consideration. And you could get a lot of the same sort of result with, say, a low base speed and a built-in hull mod that just amplifies the zero flux speed bonus.