I get this problem both in the Unity desktop environment and KDE Plasma. Some entries in the global menu are missing when I first open the application. After switching to another window and coming back they finally appear. Here are a couple of videos to show what my problem is: in Unity and in KDE Plasma 5.13.I assumed this is a problem of your program and not of the global menu because I don't experience it in other gtk apps such as Libreoffice and GIMP.
Which version of Sublime Text are you using? We made a switch to GTK3 in development releases which could be the solution or cause of your issues.
I'm using the stable version, build 3176. I'll try the dev build and report back.
EDIT: I don't have a license so I can't do that, but thanks anyway.