PR 7272188 was submitted reporting a regression from NX9 to NX10. In NX9 you could correct the order using a Drafting Parts List from which a MW BOM could be created. Not the case in NX10.
Here was the explanation from development. The PR was converted to an ER.
In NX10, we designed a new BOM function to replace the old one. In the new BOM function, we do not use the PLIST to generate BOM anymore, so any changes you make in PLIST will not be reflected to the BOM UI.
There are two ways to resolve your problem in NX 10.0:
1. You can get the old BOM function back by setting the option in the Customer Defaults (File > Utilities > Customer Defaults > Shared Tooling Options > Bill of Material > General > Use Legacy Command).
2. You can correct the order manually in the Excel window during your export procedure (NOTE: The changes you make in Excel window will not be retained and reflected to the BOM UI too).
This problem will be resolved thoroughly in a future version.