It depends on the software. Windows has a built in layer called WASAPI (Windows Audio Session API) that software can use to bitstream.
In @rick3r 's case he'll need to change the settings in Plex to get this working. If it still doesn't, he may need to update his chipset and video drivers...
Welcome to the forum Eric. You've got a whole mess of problems below, so I'll answer them individually. I'd start with a factory reset on your AVR, and then manually upgrade the firmware using a USB to RS232 adapter. That should get you in better shape to resolve the rest of these issues...