IIRC, the change log states that organization of M4A files are not yet supported :

http://openbossa.indt.org.br/canola/using.html

My [FLAC, M4A, AAC] music doesn't get organized! Sorry but we are also adding support format by format. We had only mp3, now we have ogg and wma and in the near future all the formats supported by the platform will be properly supported inside Canola.

It's kinda useful to read the developer's page on known issues before you blindly install software, just so you don't get any surprises