FlashVSR alters the audio codec.   Why?

Before upscaling, my video has audio in vlc player and avidemux and audacity.
After upscaling, my video has audio only in vlc player.
No audio in avidemux, and audacity just has loud static.
Your upscaler seems to be converting the audio codec.
Is this a mistake?
Can you update it so it does not do this?
It is inconvenient to have to use ffmpeg to fix it afterwards. 