It seems to work perfectly fine with 1000 munitions in storage. However with 300 munis in storage it only drops the initial 15 shells. Seems like a code hickup where it takes the remaining munitions (stockpile minus 180 mu ability cost) to calculate the extra shells rather than the total that was in the bank at the start.
If Relic ever lets us do another (bugfix) patch, we'll have a look at it...
Though, wouldn't it be preferable to have the ability drop a fixed amount of shells? I mean; i'd rather have 180 muni for 15 shells then 300 muni for 24 shells from the same ability (since you can't control exactly where the ability stops). Would leave room for other muni abiliies instead of draining your banked amount.