You need to check the Network Type Parameters configuration. There are 3 settings to check. The Settlement Rule Strategy assigned, the default settlement rule and the indicator for the Activity Account Assignment.
If you have selected to do the Activity Account Assignment then each activity is indivudually assigned to a WBS element. If it is off then only the Network Header is assigned to a WBS and all activities use it.
From what you wrote you should not be doing activity account assignment. You want to settle from the Network Header.