It sounds like he just read the Pro Keys chart off the video and played it on a standard keyboard.
Kurio, don't feel too bad about being off , since apparently it was rather consistent. Thirds (major) and fifths are mathematically standard ratios of the root (1.33 and 1.5, IIRC), and it's common that incorrect notes fall around those intervals.
Yes, being 3 semitones off is something that actually happens more often than one would think. That interval is used in minor chords, major chords, and also is the difference between major keys and their relative minors.
It is disappointing that Chuck Berry wasn't happy to go with Rock Band. (unless he feels he wants to be approached by them themselves). Well done on getting Bed Intruder. Hopefully you'll be able to somehow squeeze Winning out of Charlie Sheen (as clearly the Gregory Brothers wouldn't be too hard to get permission from, as you've worked with them already)