Yes, Console does show a permissions problem:
4/19/13 8:56:17.102 PM Alfred Assistant[567]: Update Alfred 4/19/13 8:56:17.176 PM Alfred Assistant[567]: Unzipping '/Users/davehein/Library/Caches/com.runningwithcrayons.Alfred-2/Updates/Alfred_2.0.3_187.zip' 4/19/13 8:56:17.953 PM Alfred Assistant[567]: Looking for instances of Alfred to terminate... 4/19/13 8:56:17.963 PM Alfred Assistant[567]: 1 Alfred related apps found, great! 4/19/13 8:56:17.965 PM Alfred Assistant[567]: Attempting to terminate '/Applications/Alfred 2.app' 4/19/13 8:56:18.589 PM Alfred Assistant[567]: Working with app name 'Alfred 2.app' 4/19/13 8:56:18.759 PM Alfred Assistant[567]: Moving Alfred from '/private/var/folders/66/845n8xtc8v5f19008k8y4ry00000gn/T/TemporaryItems/(A Document Being Saved By Alfred Assistant)/Alfred 2.app' to '/Applications/Alfred 2.app' 4/19/13 8:56:18.760 PM Alfred Assistant[567]: Unable to replace: You don’t have permission to save the file “Alfred 2.app”. 4/19/13 8:56:18.760 PM Alfred Assistant[567]: Cleaning up temp folder 4/19/13 8:56:18.784 PM Alfred Assistant[567]: Restarting '/Applications/Alfred 2.app' 4/19/13 8:56:18.917 PM Alfred Assistant[567]: Deleting update zip
The "Alfred 2.app" folder is owned by "datihein:staff" which is a normal user account, and is probably the account I used when I installed Alfred 2 (I have Alfred 1 on the system as well). I'm certain I was prompted for an administrative userid (which would be required to write into the /Applications folder). My admin account is "davehein" and most software gets installed as "davehein:admin" or "davehein:davehein". (aside: on my system "root" belongs to the "admin" group).
So, I naively did a "sudo chown -R davehein:admin Alfred\ 2.app" and tried the update again. This time it worked.
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Dave Hein