I upgraded to Yosemite yesterday on my MBP. I'm running Alfred 2.5.1 (306).
At first it was working just fine, but I noticed it wasn't finding 1password 5 as I type commands into the Alfred window. I usually would get 1password to show up as soon as I typed "1" or "1p", but the only thing it was showing is "1Password Bookmark...". It would never show the app itself, which I wanted to launch as opposed to looking up a bookmark.
So I went to Alfred preferences, and cleared the Application Cache under the Advanced tab. Didn't help. So I rebuilt the OS X Metadata index, deleting the Spotlight index in the process. It ran for hours yesterday evening, all night, and hours more this morning and it still didn't fix it.
Oddly enough, it I use Spotlight to try and find applications, it's not finding those either. So I'm thinking it's not Alfred, but I can't be sure since I have never one used spotlight since I first installed Alfred a couple versions ago.
Any thoughts?