Either ID3 or APE should be supported by Mp3tag, make sure to have set the correct reading and writing options under Mp3tag/Tools/Options/Mpeg.
As described there ... near the bottom of message #13 ...
Wie vorgehen um doppelte per %_md5audio% finden
... use e. g. FormatString: %MY_MD5AUDIO%|%_PATH%
... or in your case: "%_PATH%","%MD5AUDIO%"
... because Mp3tag needs the full path to identify the file.
You have to adapt the mte report file too.
DD.20110206.2104.CET