The balloons of a BOM refer to the active model on each individual sheet. In other words, when you insert a BOM into a sheet, the program will insert the BOM referring to the model that is active on that sheet. If that model is different than the active model on the other sheets, then you will get different balloon numbering.
In order to get the same numbering sequence, I insert the same model on all sheets, then insert the BOM. I then hide the view (if I don't need it), and place detail views, etc, and insert balloons as needed.
You can also manually modify the balloon number by changing the number system to 'custom'.
Hope this helps.