s6a9d6u9s

Are you just doing a plain attack initially, and then shift + attack for all extra commands? If you do shift + attack from the beginning they may just be wanting to finish killing their current target before they start following your commands.

You can self destruct ships but you still have to hurry and build more before the slots fill up again. It would be nice to be able to disable/enable the ability at will though, but I guess that might piss off the ghost fleet or whatever :P