Note:  This article is specific to Bentley Map V8i.

Bentley Map V8i (SELECTseries 4) doesn't appear to honor the Use color table preference for references. This can be resolved by adding the following variable to your UCF:

MS_REFCOLORTABLE = 1

An alternate solution is to locate and open  ...\config\appl\msgeo.cfg. Navigate to Line 386 and comment out MS_REFCOLORTABLE = 2.  This is done by preceding the line with a #.  This ensures the variable is not read and is therefore undefined.  When undefined, Bentley Map will honour the Use Color Table preference. 

Additional Information:

MS_REFCOLORTABLE determines how the Use Color Table preference is used.

MS_REFCOLORTABLE = 1  MicroStation always uses the reference's color table. 
MS_REFCOLORTABLE is defined and set to any value other than 1 - MicroStation never uses the reference's color table. 
MS_REFCOLORTABLE is not defined -  MicroStation uses the user preference to determine whether or not to use the reference's color table.