Hmm... I've been researching and pondering your issue, and am sadly no nearer to finding an answer. I fear this is something I'm not going to be able to help with, but I do have a few suggestions on what to do next.
In addition to the things I've already suggested (that you haven't already tried), try completely removing all traces of the audio drivers (uninstall and then use some variety of driver sweeper to make absolutely sure) and then reinstall them once again. It could be related to a corrupted install that doesn't get removed properly during a normal uninstallation.
This will be annoying, I know, but try going over every component and program relating to your audio once again with a fine tooth comb. A long shot, I know, but I've been saved myself by going back and having one more look.
I haven't seen anything obvious in the more recent BIOS releases that would apply to your particular sound issues (BIOS updates normally fix hardware issues, and yours sounds more like a software one), but you could consider updating to the latest version, as a last resort (again, you don't need to, and if you're not comfortable doing this, you shouldn't).
To go along with the last one, you could think about reinstalling Windows and starting again from scratch (a common route to take when people exhaust other easier options). But again, you don't need to do this, and could/should probably skip to my next point before doing this one.
Regarding what to do next, besides trying again on the forums here, the MSI forums might help, as there are a lot of people with very specific knowledge of their products there. You may also need to think about contacting MSI's technical support as well; I haven't had any personal experience with them, but I believe they're meant to be reasonably good.
If all else fails, sadly you may need to return the motherboard (either to where you bought it, or a warranty claim direct to MSI) and get a replacement; it's possible it really is a hardware issue.