In JUCEApplicationBase::initialiseApp() there’s a bug caused by lazy evaluation:
if ((! moreThanOneInstanceAllowed()) && sendCommandLineToPreexistingInstance())
This means that sendCommandLineToPreexistingInstance(), which creates multipleInstanceHandler, only gets called when moreThanOneInstanceAllowed() returns false. This then causes anotherInstanceStarted() not getting called, and probably other issues as well.
I do use a bunch of customized standalone related classes, but I’m pretty sure I’ve identified this bug correctly.
Simple fix - reverse the order of the evaluation.