I've noticed that apps such as 1Password that use the "modern" method of Login Items, where there's an app bundle in the main app's LoginItems folder, do not consistently re-launch after a reboot, especially after a restart triggered by installing an OS X security update. 1Password is one such app, and in fact it didn't relaunch after I applied the last security update a few days ago. But sometimes it does relaunch, and other apps don't. On the other hand, this morning I shutdown and restarted, and everything launched.
Do you have any idea what's going on here? Is this truly random or is there some hidden consistency? Is it an OS X bug (I'm on 10.10.5), or is it a problem with how the code is enabling the login item, or both? It's like whatever it is doing to set the login status as enabled isn't always sticking.
FWIW, I have 4 modern login items enabled (1Password, Amphetamine, DisplayMenu, Revisions) and I think they've all failed to launch at least once.
1Password Version: 6.3
Extension Version: Not Provided
OS Version: OS X 10.10.5
Sync Type: Dropbox