It's only a minor little thing, but U2wanderer.org picked it up in their documentation of this Best of's "Mysterious Ways" lyrics: Right before the second chorus, whereas the Achtung Baby version went "She's the wave / She'll turn the tide / She sees the man inside the child, yeah," the Best of 1990-2000 version goes "She's the wave / She'll turn the tide / And no questions, she knows why."
Nothing big, I guess... but do you see any significance to the altered verse?
BTW, that was a great find in your last post, Hapavox!