Departments will not go to handheld devices unless an asset created on the PC has a department associated with it when you create the mobile database. If you create a new asset or edit an existing asset and include a department in the field, that department information will be sent to the handheld device. However, if you create a new department and don't use it with an asset anywhere it will not go to the handheld, even if you create a new database for the handheld and send it to the unit.
If you enter the department either manually or via scanning a barcode for the department the value will upload to the PC correctly. This is true even if the department doesn't show up on the handheld when you start.