Working on a client's instance today, it was brought to my attention that the top level menu items (Dashboard, Open, Search, etc) were being included as items in the Open menu. The menu.xml file is one that was customized to call the client's Project Issue, Risk, and Scope Change request types instead of the OOTB RTs. In the $PPM_HOME/conf/menus directory was the modified menu.xml file and a backup copy of the original menu.xml. After hours of trying to figure out why this was happening, including searching the wealth of knowledge in this community forum, a colleague working for the same client came in with the solution: there can only be one XML file in the $PPM_HOME/conf/menus directory. We moved the backup file to another location and bounced the server. Now the menus are behaving as expected with no extra menu options displayed.
Re: Quick Tip: Backing up and editing menu.xml file
Jason - interesting. I've got a similar setup with custom menu items for those entities. After upgrading to 9.12.0005 (from pl3) the proposal one is broken, even after copying my original menu.xml back. The menu item works - it calls the right RT - but the text label isn't picking up the right value from my .properties file...it just says entities.proposals
I know I have some backups in that directory, I'll clean it up and see if that makes a difference.