I've worked on two projects so far and it's happened both times. The first project was using ProRes source footage and then outside video assets were brought in that were H264.
Now I'm working on a project that is using Canon DSLR H.264 native footage and video assets that are in H264 and a few that are XDCAM EX.
Also using many still images but it seems as though it will happen randomly when I load a video clip into the Source window. The video clip will play with audio in the source monitor, but then when I bring it into the timeline this is when the entire system audio will drop out and mute entirely.