digikam from trunk : reverse RAW file generator source code about thumbnail rotation. I suspect a problem in this code witch broke CR2 file thumbs and don't rotate properly thumbs (certainly some camera tags orientation flags without respect TIFF/EP spec).

Alternative solutions for the future :

1 / using future libopenraw library from freedesktop.org (http://www.freedesktop.org/wiki/Software_2flibopenraw)
2 / using Exiv2 thumbs extractor when TIFF/EP will be finalized (my prefered way (:=)))