Hi and welcome to our forums.
By default, a custom action should be automatically added to any new build. However, it may not work in one build if the files it references are excluded from that build or if a condition that includes only some specific builds is set on it (e.g. AI_BUILD_NAME="DefaultBuild").
In order to be able to investigate your problem please send me the .AIP (project file), the problematic custom action and buld's name and a verbose log
of the installation to support at advancedinstaller dot com