The exact same thing just happened on my Mac mini with Alfred installed. It froze right before the login screen, and when I disabled Alfred login, it began to work.
Then just now, on my MBA, it froze until I restarted. After logging in, I opened Alfred to see that it it was autostarting at login. I thought I had disabled autologin, but I think that b/c of your reply, I turned it back on thinking perhaps it was truly a red herring. So when it just froze again, it seems too coincidental to be a red herring. It's happening on two of my Macs, each time it happens only when Alfred autostarts. Each time the froze doesn't occur when Alfred (and only Alfred) has been turned off.
Please look into this, as I've provided a lot of data for you to start exploring the issue.
If OS X permissions is the culprit, how would I repair it?