I'm having the same problem and I am using IDE version 1.2.4... I'm running Windows 8.1. Is there a fix for this?
Are you right clicking in the Menu Designer (which you get by double clicking on the TMainMenu component) or are you right clicking on the TMainMenu itself? Reading through this thread, I'm unsure if there's any actual issues with the Menu Designer been encountered...
Oh wait... Ahh.... There is one scenario that makes sense
Under the following sequence, no new MenuItems will be added. This is a (newly) known issue, and the patch has already been created and is ready for adding to trunk:
Open the Form in the designer. Don't change anything else. Double click on the editor. Do some work in the Menu Designer only (don't touch the object inspector). Everything looks good in the Menu Designer. Close the Designer. Close the form, close the unit. Re-open the unit, none of the changes were saved.
Is the above roughly what was happening?
Under a series of circumstances (Right Click on a Menu in the designer, choose Move Up/Move Down for example, but these weren't the only ones), the Menu Editor was not notifying Lazarus that the form had changed. Once you closed the Menu Designer, Lazarus still has no clue that changes have been made, so when you closed the form/unit, you weren't asked to save changes.
If this is the case, then the workaround for now is really easy. Close the Menu Designer. Move the form in the designer to a new location (even by one pixel). Now Lazarus knows the form has changed, and when you close the form, you will be asked to save changes. And presumably this is why this went unnoticed for so long. When working with Menu's, people usually make other changes to the form as well (including rename Menu Items) which was sufficient for Lazarus to know changes had been made.
As I said, a patch for this has been prepared (including a series of other minor improvements/fixes to the menu designer) and will be uploaded to Trunk sometime soon. (Lazarus Developers are waiting on me for some clarifications on tangentially related issues)
http://bugs.freepascal.org/view.php?id=26795