No menu bar-based applications will re-open on restart, 10.8

I got a Late 2012 iMac in December of 2012. I have had one persistent problem since then. When I restart the machine and the OS resumes where I left off by re-opening apps I had open as the machine restarted, everything will re-open except for any application that exists soley in the menu bar.  That's all I can narrow it down to. Applications that do not re-open 100% consistently are:
- Air Video Server
- Fantastical (Mac App Store)
- Menu Bar Audio (Mac App Store)
- Alfred
And these ones vary:
- Dropbox
- Tweetbot
It gets weirder.
I have all of these items in my login items. Well, I have had them there. When I restart (either with a resume or when I disable that, booting from scratch), the items don't launch and they're removed from my login items list. I've seen this happen at least a half dozen times. I can re-add them and restart, they'll be gone again (this happens with about 50% of restarts).
I've tried:
- New user account
- Complete disk wipe and OS reinstall (not restored, fresh install)
- Booting from safe mode, removing login items, booting normally, re-adding, restarting again
- Every version of 10.8 since I got the machine - 10.8.1, .2, .3
I completely stumped Apple phone support for hours a couple months ago. I don't have the hours now to try that all over again, and my 3 month phone support limit is up .. so I'm trying the community. I'm completely stumped.
Anybody experienced anything remotely similar?

Hello,
Open console in Applications>Utilities, check the system log for the date/time of the last problem  & the Startup right after that for clues.

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