using custom colors causes plotting to pen 1 by default
Entity color pen mapping changes to pen #1 if changed from the defaults. Pen mapping should not change if the entity changes. Geometry map to pen 1, letter to pen 2, etc regardless if the geometry is black, white or anything in between. the current work around is to specify the rgb values in a pen table. Editing a pen table every time someone wishes to change their color schemes in not very efficient.
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Here are the actual articles and the related SPRs. The specific issue you mentioned is the second one in the list below. This effectively kills a users ability to use a custom system colors file while still allowing the system to reliably print in color. Changing the underlying RGB value of a system color (to accommodate a user's display preference) shouldn't alter the actual plot output!