mkvtoolnix is a set of tools that allow users to display information about, extract streams from, merge several streams into, and split Matroska media files. Supported video stream types include streams from AVIs, Ogg/OGM, and RealVideo? files. Supported audio formats include Vorbis, RealAudio?, MP3, MP2, FLAC, AC3, and AAC. Several subtitle formats are supported, including SRT, SSA, ASS, VobSub?, and many others. The resulting files can be played back with various media players on Linux/Unix? or the Matroska Direct Show filters under Windows.

mkvmerge

If you want dual audio without problems, remux the AVI into a container format that supports multiple audio tracks by design and not by hacks like the 'Morgan stream switcher' or MPC's audio switcher.

MKV or MP4. Download the  mkvtoolnix installer. There's a program called mmg.exe (mkvmerge) included. Use that for muxing.