There are many X client applications that use the standard or default X
color map. MacX uses the standard Macintosh System palette as the default
color map (which it should), though this can lead to the situation you
describe. The System palette has 128 colors locked in and no additional
colors specified.
If you, using the X client application, request a new color map from MacX,
you should get all 256 colors.
In MacX 1.2 loading the standard color map is an option in the display
preferences dialog.