File sizes greyed out (strange extended attributes) in Finder on Lion?
I have only the craziest of guesses, but since we're all striking out so far, here goes.

Is there any chance you've turned on the Asepsis mode which installs a kernel extension? You may have not disabled that in your testing (a safe boot should confirm / rule this out as well). It seems possible that it's intentionally showing you which folders it has replaced the normal .DS_store file with entries in /usr/local/.dscache

I would also use mdls to inspect the metadata for these folders (since apps are really folders these days) in case some clue jumps out at you.