Well, I've decided to put this thread here to benifit you lot! The best way to get around these annoying bugs in XP and 2k is simply to cheat!

In-game, press Ctrl + E. You should hear a beep. Then type in "battlecheats" (without the quotes). A dialog box should come up saying "Mode on".

Then, jet off to your pirate base/alien probe.

Then, when you start the mission, target the object of desires, and hit:

Alt + ¬ on UK/European keyboards
or Alt + ~ on US keyboards
(In any case, its the button directly below Esc)

WARNING: For some reason, when the thing goes boom, your ship goes all funny (as if it has died), and stops moving so just press H to go into hyperspace. It may look strange, but you aren't affected in anyway. It might be wise to destroy all covering ships in the pirate base attacks before you blow up the base.

Also note, that probes that have enemy craft spawning there when it is blown are also "invisble" at -0.00km, always behind, so simply blow them up to.

These are the only cheats I'm telling you because they're the only ones you need

Arent there -anny- real fix for that bug?
As i cant realy disable and tow a probe that way. (if i have to do that)
Hmm, wonder where that button is located for me.. :-/