Are you working with any custom configuration?
Look into your SS3 (and or SS2) Common Files\Bentley Shared\Civil Platform\08.11.09(Bentley Civil Commands.cfg) be sure the following lines are commented out:
# %level 2
# %if !defined (MS_DGNAPPS)
# MS_DGNAPPS : $(BC_ALL_ASSEMBLIES)CivilDialogExt.ma
# MS_DGNSET_APPS : CivilDialogExt
# MS_USERPREF_APPS : CivilDialogExt
# %endif
#%level 1
Hopefully this will remove the second instance