This has to have to do something how the background ambience sample is being played. There's no completely silence, but a soft humming ambience constantly in the background.
It's "ambience.ogg" sample in audio/ folder, if you want to check it out.
As the issue changed with Tinker updating library files is refers to problems in playing that sample in SDL or SDL_mixer libraries.
weakend2k13's sample has got a quite disturbing crack, which I can't explain in any way. It's cycle doesn't meet eg. the duration of the ambience sample.
What both of you could try though, would be to simply delete ambience.ogg from audio/ folder and see if it makes a difference.
The game will notify of ambience.ogg loading problem upon start, press a key and it continues.
In any case, there are no code changes to audio handling from our behalf, so this points to system/SDL2/SDL_mixer oddities.
And as the reports of it are this little it's also likely a very rare oddity, which is difficult to exactly pinpoint or remedy.