MiLkMaN859 :
It shows sounds is plugged in and playing in playback devices. No sound comes out when I test speakers even though the green bars are lighting up in playback devices. Sounds will randomly come and go. Mostly no sound. I switched the connected from optical to an aux cord and same issue. I hooked up a small battery operated Bluetooth speaker and ran an aux cord from the back panel sound and it is NOT cutting in and out and works fine. Any thoughts where the problem might be coming from?
The receiver has its own built in devices, updating your computer audio devices is not necessary (with your HTPC setup). You've stated that you have tested your speakers and noted the green bars, which I assume is in the (control panel's) Hardware and Sound. Use your Onkyo HT-R390 remote control and press setup/ 6. Level Cal/ and press select there you will see your 5.1 speakers and can navigate through each of them. You should hear white noise while you're in this section. If not, exit from this section. On the dashboard of your receiver hit the VCR/DVD button while pressing the power button at the same time, this will reset your Onkyo to its factory default settings. Unplug your machine for a minute now. Plug it back in, wait a minute for the HDMI board to warm up, navigate to 6. Level Cal settings and if you're able to hear the white noise you "might" be in luck. I'm going to be the bearer of bad news and inform you that the Onkyo HT-390 (HT S3400) was recalled in lieu of quality issues:
http://legacy.onkyousa.com/press_releases.cfm?id=253 [Source]. If all else has been continuing to fail since the time you posted, I suggest reaching out to them, it will be a fight and you will probably get turned down a few times, don't give up, best of luck.