Are you using the Mission Editor for your edits, or a text editor John Pancoast? The ME has a tendency to put things the way it wants them, not the way you want them (kind of like Windows does
). 500m is the "default" spacing for ships, and planes are at 300m. If your ships are all at 500m, your planes are probably now set to 300m also. If you use a text editor and do a Search and Replace, you would have better luck with it staying the way you want... usually... Search and Replace can be your friend, but it can also be your enemy if you don't want all occurrences of something to change...
Edit: forgot to mention... If you have RGG (Random Generated Groups) in the scripted file (Campaign_SCR) or scripted Groups / Units in the RGG file (Campaign_RND), things really go wonky when you use the ME...