Hello @NAVData
The issue is not caused by the lack of an ICAO Ident in the custom waypoints. This is just a workaround.
The root cause is an issue with how the waypoints are processed when BGL contains (probably ends up with) <Airport> elements with the onlyAddIfReplace attribute set to true.
I have logged a bug for this.
The problem occurs when these are processed last so it would be interesting to check if such elements are defined at the end of your BGL files and if moving them at the beginning of the file solves the problem.
Regards,
Sylvain