I found a solution to this problem.
From the edit menu, select "Volume and Balance..."
This brings up a window with three volume level bars. The first is for the "Main Video" line, the second is for the "Video Overlay" line, and the third for the "Audio Mix" line. If you take the middle bar and drag it to zero, it seems to fix the issue. Strangely, after you put it back to 100 it still seems to be keep it going at the correct volume level. Perhaps playing around with these volume level bars "resets" how the program looks at volume?