Exporting to a Geodatabase

When exporting a Map SS4 file to a Geodatabse we're finding the resultant GDB doesn't just contain datasets for the Map file being exported but rather (empty or otherwise) datasets for ALL features in Command Manager. In our case this is resulting in hundreds of extra pieces of information. Can't see any way of turning this off?

As an example, our Command Manager has hundreds of features and Services' are grouped separately eg. 'Drainage', 'Electrical' etc. Our base files are simarly organised with separate base files for each service.

If we go into Map, attach just the Drainage file, do a standard geodatabase export and then look at the geodatabase with the free ArcGIS Explorer utility, it seems to know about ALL features contained in Command Manager(Drainage, Electrical and the hundreds of other features) rather than just the Drainage information. It doesn't contain the graphics for the non-drainage info. but all the information is shown,

Any one know a way of turning this off as part of the export?