what kind motherboard? I'm assuming that you are using the hdmi port on it to go to the AVR? Or are you using a video card with hdmi?
Also what does the AVR "see" the signal as on the front panel? Because if it see "stereo" while playing mp3s then putting it into Dolby Pro Logic II music mode all you need to do.
Most lickly you are already feeding it a PCM signal since the mp3 in not a bitstream source and unless the sound from you hdmi port being encoded to Ac3 or DTS it is just PCM.