I have also reviewed the source code ... from my dev site and the fresh install from today ....
line by line comparison of the two would be in order. If you use BBEdit on the Mac you can automatically compare for differences.
If one works and the other doesn't then you have at least one difference.
Nothing stupid here? You're not editing offline and uploading to the wrong directory? We've all done it.
Is your server caching something? I've seen where I've made changes but the system behaves the same as before. After a while, it catches up but not after I've changed it back... adding great frustration and confusion.