Well, MC would be using different DirectShow audio filters, which could explain the lack of audio when 3D plays for a short while. It could be that the better audio processing in MC is using just a bit more CPU power and tipping the i3 Skylake chip over the top, so it can't cope. Or it could be that MC just hasn't synced up the audio yet and started playback, and when it tries that is the cause of playback stopping. Sometimes there is a short bit of no sound before playback starts normally.
Does the CPU, GPU, or memory usage peak out when you try to play 3D?
That could be down to the source video, so you will have to explain what that is. A Blu-ray disc? A Blu-ray rip? If so, what format rip? Full folder set, ISO, MKV? Did you do the rip? etc. Are you using the Blu-ray menu or just playing the main title? What audio formats does the source have, and what are you trying to play? Just plain old 5.1 channel PCM, or are you Bitstreaming? You said you tried DirectSound out so I assume PCM, but you didn't say when you tried outputting to the Receiver if you used WASAPI Exclusive or ASIO.
Also, how do you connect from the HTPC to the Receiver, via HDMI? Then output video from the Receiver to the TV via HDMI out on the Receiver?
You are obviously still make changes in the madVR settings as well, since you mentioned trying fullscreen exclusive on and the fullscreen exclusive off. I'm pretty sure resetting madVR to defaults and using JRiver Quality Settings would leave Fullscreen Exclusive mode off. Use the JRiver defaults, and as you have an iGPU, use the Quality Setting of Best Performance. I don't use Fullscreen Exclusive and haven't for some time. 3D works fine without it. I think that was discussed in the threads I linked to. It has certainly been discussed a lot and I think the conclusion these days is to leave it off. But I am using a nVidia GPU.
It sounds like that is getting you video in 2D now and audio working. I assume that you have ticked "Enable 3D Blu-ray and MKV 3D decoding" in MC. Also that if you are opening madVR settings you are doing it through MC Options pages, or right-clicking a playing video. Know that JRiver uses a different version of madVR to other available versions, and that it has special handling in place for OSD overlays and such. JRiver doesn't support madVR tuning, and recommends using their presets. I'm certainly no madVR expert. So what I suggest is getting MC set up for 3D as per the defaults and Hendrik's instructions in the thread I linked to, and then if that just plays 2D, but with sounds, we debug that.
Maybe try catching a MC log of trying to play a 3D source, and see if there is anything in there that points to why you are just getting 2D.