If you've encountered some issues and your preferences have become corrupted, you may need to reset Alfred's settings to defaults.
To do this, quit Alfred first, then delete the following files/folders from your user directory. You may wish to delete the first three and see if behaviour is back to normal, as you may not need to delete your Application Support folder.
~/Library/Preferences/com.runningwithcrayons.Alfred-2.plist ~/Library/Preferences/com.runningwithcrayons.Alfred-Preferences.plist ~/Library/Caches/com.runningwithcrayons.Alfred-2 ~/Library/Application Support/Alfred 2
When relaunching Alfred, you will need to set your hotkey and locale again, and your preferences will be back to Alfred's defaults.
If you are using Alfred's syncing feature, you'll find these files in your sync folder (e.g. within Dropbox)