I can confirm this problem.
You should really report such things in the official issue thread here: https://forum.reallusion.com/Topic224537-385-1.aspx, otherwise they may not get noticed.
I'll create an entry (DONE).
Meanwhile, as a workaround, I found that you will get correct stereoscopic output when you render to an image sequence. The recommended format to use is PNG, which gives the best quality at reduced size.
The image sequence can then be loaded in a video editing program and will act as a regular video file. You can capture any sound and music from iClone by rendering to a WAV audio file and then use that in the video editor.