I had a similar problem today. I have Things.app, and I prefer to launch it with "h". Andrew, your explanation about adding a Spotlight comment fixed it for me. Glad I searched a bit before opening up a new topic. It's been driving me crazy for a long time, and I finally decided to fix it. I suggest adding it to a FAQ or some other help location such as this:
http://support.alfredapp.com/kb:indexing
Although I won't forget it again, and will be adding lots of comments now. Thanks again!