There are no line separators in the root main menu, but there are a few inside sub menu "Current" which is after the column. Not sure if that still causes issues or not.
Either way removing the column separator and adding it again seems to have solved the issue. I no longer have to restart QAP to get the column displayed after changes.
The greyed out live folder was unrelated, seems to be caused by the option
Refresh this live folder menu only with the command "Refresh Live Folders and Shared menus"; disabling it no longer leaves it greyed out after saving changes.
Thanks for the quick reply, the issue seems solved from my part.
Appreciate the support.