asportnoy

I did intentionally update it and I do want it to continue updating, just don't want it overwriting those things.

I'm using some workflows from the beta gallery. For some of my workflows, I like to have a custom icon instead of the default one. However, updating the workflow overwrites my custom icon. It would be nice to have it not overwrite my custom icon when I update, or at least prompt me first. I also have custom keywords (instead of the default) for some of the workflows, so having the same behavior there would be great.

Maybe Dropbox is having a hard time handling the permissions because it's inside Alfred?

I'm getting the same issue. While troubleshooting, one of the errors I got mentioned something with a uid (user ID). My guess is that Dropbox is not properly setting the permissions of executables which prevents them from being executed (inside of alfred or directly from terminal). I tried playing around with different chmod / chown settings to see if I could get the settings back but no luck. If I copy the preferences over manually from my other mac then they will work. However, then dropbox syncs the updated version and it'll stop working on the other mac. So doesn't seem like there's any option besides turning off Dropbox syncing. I have other executables being synced by Dropbox without issue, so I think this is something specific to Alfred.