The modifier order is as entered.
You can change the order by removing them all and re-entering, or changing the names in the database [MenuItemProperties], logout of SambaPos and log back in to reload the database.
The database should only be modified if you want to change the order - do not try to add more modifiers or you risk corrupting the database.
If you are talking about adding multiple modifiers to an item, then yes the order is as the order the modifiers where created, and does not change.
Emre, this is a bug.