Are you watching a 3D mkv rip? Is it side-by-side or under-over? In this case, it is seen and played as a normal video file and converted by your 3D TV. There is no need to use the 3D button on the remote.
It should work fine if you use the standard "wrapper" settings as this shells Kodi out to "external videoplayer" and then AAC 5.1 is passed through as PCM audio to your AVR.
If you were trying to watch a 3D full frame-packed MVC .iso file (which is unlikely as I've not seen these come with lossy AAC audio) try using MediaCenter for playback rather than Kodi. If you have not already done so, it is worth installing the Blu-ray menu add-on for this situation (to get the full menu

).