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Problem Description:
Bentley Map SS4 doesn't seem to honor "Use color table" preference for references. If DGN file is opened directly colors are correct but when attached to DGN with different color table it shows wrong colors.
Workaround:
Comment MS_REFCOLORTABLE variable in msgeo.cfg file.It should display colors of reference file according to "Use color table" preference.
Source :http://communities.bentley.com/products/geospatial/desktop/f/5924/t/126816#pi20068filter=all&pi20068scroll=false