Sfon: I encountered a nasty bug making this mission impossible in FSOpen.
Seems at least the cruisers and up require scanning to be done within range of a point at their front, rather than counting distance from the whole ship. This makes the second to last ship very hard to scan, and the last perhaps impossible.
I went back to normal, non-FSOpen Freespace 1 and am no longer having this problem. Scanning is easy now, though I still have not been able to survive jumping out :(
This not a bug, well, not technically.
You need to turn off auto sub-targeting (Alt + S). What happens is that instead of scanning the target, your ship tries to scan the subsystem, which, on the Eva and Lucy, could be more than a kilometre away from your position, even if you're next to the ship.
Auto sub-targeting is turned off by default on retail FS, which is why you are no longer encountering it.