The original spec didn't allow for anything but "dark on light" codes. The official spec has been amended a bunch of times, but it's not always clear what version of the QR code spec an app uses. If it stuck with the original from 2000, it can't scan inverted codes. The spec itself has been amended in 2006, but the full spec is proprietary and needs to be bought, so not everyone may have updated their code if they have the old spec on a network share somewhere.
