Well, you are right, there may be one or more small bugs in Mp3tag FLAC related code.
There are differences between example 2) and 3) in spelling resp. casing the tag field labels.
Album/album
Artist/ARTIST
Title/title
This should not happen.
It seems that Mp3tag does an alphabetical sort on the tag field label names.
Maybe the sorting algorithm lose the last resp. first element
(this might be something of Florian's peculiarities, struggling with zero based arrays ... hey Florian, don't worry 
)
T. A. G. Ger, I think you should make a note in the bug forum.
DD.20080923.1527.CEST