We need to know how you recovered your files..
Did you use Migration Assistant or some other method?
Was your computer running the same OS before and after you wiped it.. in other words are the versions of mail identical??
If you changed version of mail then various things can happen.. it also depend if you restored not just your files but settings as well.
Some of this might still be too hard to answer.. recovery of files is not going to restore things identically if you didn't use a software that is called a cloner.
Some of what you did might work but it will not end up with the same layout in a different computer.. which is effectively what you have now.
There might be some clues here to help.
http://pondini.org/TM/15m.html