Custom coordinate systems are stored in DTY file(s) which need to be specified by the configuration variable MS_GEOCOORDINATE_USERLIBRARIES
In the UCF or other location, define MS_GEOCOORDINATE_USERLIBRARIES = "library[Name]"
Where 'library' specifies the filename and [Name] is the name of the root node for that library in the user interface.
MS_GEOCOORDINATE_USERLIBRARIES = d:\Project_ABC\CoordinateSystems\ProjectABC.dty[Custom]
Separate more than one with a semicolon.
If no directory is specified, the directory specified by the MS_GEOCOORDINATE_DATA is used.