This is just a first guess, but I'm wondering if you have an owner who is very hand's on/controlling (sorry, I'm forgetting terms right now, not in front of game, but I think the terms I am using are actually more diplomatic then the term in the game.)
I know the owner of my team in my fictional universe controls certain aspects of my budget and won't relinquish control to me as GM/Manager.
Now, why your owner (if it was him, and not something else causing this) would choose to put all of the budget into one area is beyond me.
Then again, I know that in the few areas (development budget and international budget) my owner controls it is clear on the appropriate screen that he is controlling it so since it doesn't sound like you are getting that message perhaps it is something else that is happening here.
Edit: Meddling. I think that's the term for my owner in the game.
