I knew that there has to be some other folders that keeps album arts.

If anyone has the same problem of changing album covers in N900 you just need to:
$ rm ~/.cache/tracker/file-*
$ rm ~/.cache/media-art/*
$ rm -R ~/MyDocs/your-music-folders/.mediaartlocal (this I think is optional but it's safe to do this)
$ tracker-processes -r

Restart device (in my case)...


Have a nice album-arts.