I ran into an issue with getting different ordered lists of departments any where that list would be utilized. When using an admin account, this list is always alphabetical. When using a non-admin account and using Department Groups and the Limit by Department option in tech permissions AND using MSSQL as the backend database, this list becomes ID ordered.
I worked with support for some time to track down this bug and it is currently on the 'to be resolved' list. If you are using one of the other DB backend types, this does not seem to present as a problem.