All,
Apparently, I must have been doing something wrong. I recreated a mission with nothing on the pylons other than guided weapons, and it worked as advertised; one per side back and forth until empty.
Sorry for the confusion. I don't know what was going on before to make me think it wasn't working. I think it may have been that I changed weapons unintentionally between firing, and therefore the different weapon fired from the same side, making me think I had just launched two of the same.
Regardless, thanks for your help and input. I'm quickly becoming quite impressed with FC2... this is a serious simulator, and one heck of a game. Easy to use, like IL2 and yet tech enough like Falcon without the sensory overload. My only wish for this game would be a new map.