Ok so I have no idea what happened. I had the free version installed. And found that very few of my videos would play on my iPhone or iPod Touch without transcoding so I purchased the Pro version (1.9.7). I installed that and got it working. Things were great for a day.
Now whenever a file has to be transcoded none of the idevices have audio. There are a few that will play on the iPad without needing to be transcoded and those have audio. Plus if I play them in a browser on a mac or PC they have audio.
If I set the media libraries to “never transcode” then there is sound, but you can’t actually watch the videos because the bit rate is too high for the connection type anywhere but the local wifi and even then it pauses once in a while.
The transcoded files all have the original M4V extension followed by a .m3u8 extension. These are the files that don’t have audio. I assume .m3u8 is the extension for whatever transcoding is going on.
I have tried un-installing (both the free and Pro versions) and then re-installing the pro version. It still doesn’t work.
The system is a Windows 7 64Bit PC Core2Duo E8400 @ 3.0GHz with 4GB of ram.