BOM Settings can not be saved. They are active only for the current session (See the CATIA documentation on this) As you have found out that if you generate a BOM on a 2D drawing, the next time the Solids are modified and then the 2D is updated your BOM reverts back to the default format as defined from Dassault.
Other than never logging off from CATIA and never sharing your drawings with someone else you could try one of the following.
When defining your BOM, (using the customize function) save the steps using the "Record Macro" option. YOu can then replay this macro each time you start CATIA up for the day.
Better yet, if you have the resources then use Knowledgeware to produce your own BOM structure.
The CATIA BOM (Along with assembly features) is one of the most unfriendly tools in CATIA. If you attend one of the conferences that the Dassault developers are at make your wishes known that this must be improved on. (In North America the spring COE conference is in March 2006)
