Also remember that the air in/out hex is a global data item, and is reset on game reload. So if you restart winSPMBT - remember to reset these to the desired values on reloading a saved game and before plotting new strikes.
If playing hot-seat against someone on the same box - then again the air in and out route may have been changed when your mate had control of the PC for his turn. So check it before plotting new strikes (or just change it randomly to do your opponent's head in, whether you have air strikes or not

!
WRT the blue on blue issue - I'd like a nice simple straight forward example save game of this (before the air strike obviously!

to debug, where the air is reasonably reliably going to do a blue on blue.
I have a feeling it is probably happening when the air strike is being plotted deep in the enemy rear zone and
possibly any off-map scatter is then erroneously being wrapped round to the players own end zone ??.
But I will need a small example savegame in order to see what the problem really is.
Andy