Custom key signatures are not applied to the right line in different clefs.
Steps to reproduce:
1 Create a score using G clef and also F clef and/or C clef.
2 Open master palette.
3 Create a custom key signature.
4 Apply it to the score.
5 The custom key signature is applied to the same line through all the different clefs. (Example: If the key signature has only and Eb and all other notes are natural. In G clef it will look and be played as an Eb. In F clef it will look and be played as a G flat and so on.)
(Tested using 3.x versions, appimage on Linux.)