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User Preferences include the Operation > Compress File on Exit option.
If selected it will only compact the file's structured storage removing elements marked for deletion.
It will not include any of the compress options found in the Compress Options dialog.
Search MicroStation help using "Compress Options Dialog" (include the quotation marks to search for the phrase) for details of the options available and related topics.
An earlier Ask Inga tip:
http://communities.bentley.com/communities/other_communities/askinga/w/askinga/configure-your-compress-options.aspx