New Mac Mini 3D Problem

That sounds rather frustrating and at best - worth a look at Plex forums.

What you might want to do if you have the resources, try XBMC via Linux or Windows and see if you still have the same problems. You should be able to do this from your Mini. There is also the Live XBMC disc that you could try as well if you have an external dvd reader.

I don't bother with 3D as I don't have true stereoscopic vision so this challenge of yours is not something I can relate to other than the typical htpc frustrations that are always there. I would also say the same for Minis with OSX not passing HD audio yet Windows on the Mini will.

Best luck to you

Hardware video decode acceleration may have been turned off for 3D.
On VLC go to the Preferences menu and select the Video Tab and look at the Output Module.

Play around with the choices to see if things change.

I want to buy exactly the same Mac mini and use it in combination with a 3D monitor, but is your problem already solved? If not I might not buy a 3D monitor....