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Bentley Map V8i (SELECTseries 4) doesn't appear to honor the Use color table preference for references.
Locate an open msgeo.cfg from the ...\config\appl\ folder.
Navigate to Line 386 and comment out MS_REFCOLORTABLE = 2. This can be done by preceding the line with a #.
Doing so sets it to not defined and then allows you to set the user preference to determine whether or not to use the reference's colour table.
Source:
http://communities.bentley.com/products/geospatial/desktop/f/5924/t/126816#pi20068filter=all&pi20068scroll=false