Gmt not reading FORMAT_GEO_MAP from gmt.conf

Not sure I understand what you need. If I run this script and comment out either of the two FORMAT_MAP_GEO statements I get what I am asking for:

#!/bin/bash
gmt begin GMT_tut_3
	gmt defaults > gmt.conf
	#gmt set FORMAT_GEO_MAP ddd.xxx
	gmt set FORMAT_GEO_MAP +D
	gmt get FORMAT_GEO_MAP
	gmt coast -R270/271/0/1 -JM6i -Bxya0.3g0.3 -Gchocolate
gmt end show

and the right answer is returned by gmt get. This is GMT 6.5 (released within a week we hope) so it is possible we fixed some issue at some point. If you can build from master then you could try.