Thats not the problem of the ammo box.
You can empty the magazine and put the ammunition into the box not the ammunition which are stored inside of the cmag or natomag.

Is it possible that you got "Postprocessing" under the video options not on "Deactivated" ?

The loot frequency depends on server settings.

This sounds to be a server problem, anti ghosting isn't activated right now:

http://forums.dayzgame.com/index.php?/topic/153994-early-access-important-information-known-issues/

This is the reason why it happened:
In the time you got the disconnect and the red font appears on the screen you have no collision detection on the server. So if you run in the direction of an wall and you got connection problems then the server calculates the way you would go if you were going. So it can happen that you spawn inside an non exisiting room like you can see on your screenshot.

Please read.
Last point in this thread:

http://forums.dayzgame.com/index.php?/topic/153994-early-access-important-information-known-issues/

Thank you