Here is what is going on.
Let’s say you are at the report level, with the type set to Budget, and a period of more then one month.
When you edit the amount shown on the report, the difference between the original amount and the amount you entered is divided by the number of months in the period, then each month is increased/decreased by the monthly amount. Simple enough. And in the case where you have a period of one year set and the original amount was zero, you end up with the 12 monthly budget amounts all set to 1/12th of the amount you entered.
But, you can end up in a dog-fight with the budget amounts if you inadvertanly edit a budget amount when the period is not set to a complete year. If, say it was set to 10 months, then any change you make will be equally applied over the 10 months, and the other two months will remain unchanged. Zeroing out the years budget amounts can be tricky too if the months are not all equal to start with. In that case whatever change you make is equally applied to the 12 months and you won’t end up with zeros in every month.
As was suggested above, don’t fight this at the report level (unless you like frustration.) Just expand into the account and go to the History view. In the 1st column set the Type to B and the Rep to M. Now you can zero out the months or set different amounts for each month without any problem.