Though it seems to me that I'm a bit late into freespace modding, I've actually stumbled upon a very nasty bug... In the disable-the-taranis mission, in SCP 3.6.5 or the latest build, I cannot target any subsystem at all, and therefore i'm unable to disable or disarm it. Also my wingmen don't obbey me when I tell them to disable theirselves. And the ship doesn't seem to fire at me at all.
I saw lurking in the forum some other guy who had the same problem. He wasn't able to fix it, though

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If you have any fix for this please email me ^^ (appart from playing the mod from the original FS2, which I don't really know how to do).