Maybe the audio driver stops sending audio but doesn’t notify AudioRelay of any error… 
Could you install this version of the server? The audio capture was slightly updated.
If this doesn’t work, could you please answer these?
- In your mind, how much time of silence is required to trigger the bug?
- Are you actively using the PC during the silence?
- Are you on Windows 7, 8 or 10?
- Are you using a laptop? There’s maybe a performance setting affecting this
- Could you provide server logs? (found through the settings menu)
Sorry for the late reply!