I found the reason why applications sometimes mysteriously get muted!
I've seen people ask many times why an application doesn't have sound anymore. I've had it multiple times. The answer is always, go to sound settings in desktop mode, open the Applications tab and unmute the application there. But how did it get muted in the first place?
I feel so stupid, but the answer is so simple that I wonder if most people don't already know it. You can mute/unmute an application by clicking the top-right area of its icon on the task bar. In handheld, I think this is so small that I didn't notice it, but finally I did.
I've wondered for a while now how some applications got into this muted state. This probably also explains why clicking an application's icon sometimes seemed to do nothing, as if the application froze. Instead, I was just muting and unmuting it!