Wordfence on "[Plugin: Wordfence Security] every PHP page hacked - but scan says all clear - how can this be?"

Do you have the following enabled on the Wordfence options page:

Scan core files against repository versions for changes

And have your core files been hacked? (You mentioned every single file)

If so then likely something in Wordfence has been modified to ignore these hacks. Let me know.

Regards,

Mark.