AFCOP - Brother AF SP here. The system that cuts the orders seems to be out of date and not very user-friendly. It has nothing to do with you being "screwed" by the folks back home at your base. When I was on active duty for Operations Noble Eagle and Enduring Freedom every single leave and earnings statement that we got said "Active Duty for Training" in the remarks section at the bottom of the LES. We were told that is just what the pay system is programmed to print. As far as the pay and benefits go, you were only down there for a few weeks so you would not be entitled to the full BAH, BAS, etc.
Bottom line is you guys dropped what you were doing in your civilian lives, went down there, worked in dirty, dangerous conditions, and helped other Americans in a time of great need. That is what being in the National Guard and Reserves is all about. You should be proud of what you did, I wish I could have gone with you guys.
Are you certain the Army Guard MP's got full allowances? In most cases you have to be on active duty for more than 139 days to get the full active duty allowances. On the other side of the coin, I heard the Air Force took care of you guys by getting you out of there on a C-130, while the Army Guard unit you were attached to was stuck waiting for days to get a train ride home. I realize that you are still fairly new to the blue, but you should be thankful for the way the Air Force looks after Airmen. There are a lot of Soldiers in Iraq right now that would love to trade their one year + deployment for an Airman's 4-6 month deployment. Be safe Airman.