According to ARSPR Ive had a related issue.
Running both Forceware 169.21 & 169.03 and fs2_open_3_6_9.exe I got this:

The newer build slightly fixed it.
Running 169.21 and either fs2_open_3_6_10-20071028T.exe or fs2_open_3_6_10-20071007T.exe I get something similar. The ship in the middle will now appear 100% correctly (all of them do), but the same ship in the lower left corner where it shows your target still suffers the same bug as before (but not all of them). Iy only happens on the ships which are well lit.
[edit]My bad, in that particular picture both ships are fixed. However the results I explained can still be seen in many other missions, for eg A Lion at the Door.[/edit]
I guess what ever was done to normal ships between those 2 versions needs to happen for target view ships? I have no idea.
Running a 7900GS, AMD 64 X2 4600+ on Windows XP Pro SP2. Want more info/testing, just ask.
Just want to add, everyone involved in updating FS2 does an excellent job. Ive never seen community support for a game like this before.