Steve -
I noticed this bug in 3.11, but I checked and it appears to be a problem in 4.0b as well. On the Combat Assignments screen, there is a bug in the missile assignment routine. I typically hit the "assign all" button, to assign the same missile to all launchers, however, I noticed when trying to manually reassign missiles by hitting the "assign" button, that it doesn't always work. It works on all launchers numbered 1-9, but any launcher numbered higher than 9 cannot have its missiles reassigned by anything aside from "assign all".
Kurt