I'm using the app "Barcode Scanner", and Google Goggles works too. But I don't think it matters which app is used.
Are you perhaps using the latest cm7 nightly? Because the latest nightly (20120409) changelog includes this entry: "disable autofocus on camcorder start", and since code readers probably depend on camcorder functionality, it may be the cause.
I'm using RC1 btw, and it seems camcorder does focus as well.