Cybersoft in irc chat on spaceempires.net took my saved game which is 1.08 patched running kwoks mod and tried it and had the same problem.
Here is the link to the saved game:
http://home.satx.rr.com/spiderwebs/Savegame.zip
I'm going to try another kwok mod game with as similar a setup i can and see if type 2 missiles will attack a planet.
Then I will try a stock game.
If I get the same issues, I'm gonna be pretty mad cuz that'd make a fairly broken game... but lets not jump to conclusions.
If somonw else wants to confirm my saved game task force 1 fleet cant attack that planet Id appreciate it.