I'm using 0.9.4931 , and the stereo issue is still there, and I'm pretty sure that the gray blacks issue is too, as it was there the last time I checked about a month or two ago.
The gray black thing seems to be due to the chip set, because my PopCornHour does the same thing (I think it is only on MPEG4 HD channels), and I think the Azbox uses the same chip set for video. I'm guessing that the audio thing must be hardware related as well, or they would have fixed it long ago. Audio is fine through the HDMI output, however.
BTW, is your computer connected to the Azbox via network? If so, you can load the firmware on the thumbdrive by plugging the thumbdrive into the Azbox, and transferring the file via FTP.