Thanks all for your answers and information, the more you know, the better.
I don't really think that the instalation folder of MeGUI is important because I never had a problem, and the volume loss when downmixing only happens with certain files, right now it only happens with this one. I have another .mkv file with a 6 channels audio that maintains the same volume when downmixing.
I moved the file to the desktop and encoded again, but I got the same result.
Here is the log:
http://textuploader.com/58uzi