Hi Andrew.
I indeed do have multiple applications run at login. Most notably Dropbox, iStat Menus and Google Japanese Language input (but for some reason the latter 2 are not listed under Login Items). Sometimes Chrome, Apple Mail, and other applications that I decided not to close before a reboot or shutdown launch via the App Resume function of the OS but I know for fact that I've enabled the first 3 myself.
I've noticed lately that whenever Alfred fails to launch, the "Launch Alfred at login" box has been unchecked. I've tried manually adding Alfred in the Login Items on multiple occasions but somehow it still manages to fail at launch randomly .
Are there any known programs that have been reported to mess with Alfred's auto launch? If so what was the work around?