Have you tried asking the developer for your money back?
I recommend searching the forum as this topic comes up quite a bit.
Sorry for the thread revival, but just wanted to note for future google searches that I did a test with Audiochecker 2.0 beta. I converted some songs that I downloaded from iTunes (256kbps AAC) to FLAC. I then used Audiochecker to analyze the files and it showed that all but one were CDDA with 100% probability. This is proof enough to me that Audiochecker is not completely reliable if you weren't already skeptical.