Yes, I've seen that issue too, but offhand I can't remember the problematic apps.
@renton, if you download and install the following macro, you'll find a technique that is fast and robust:
You'll want to replace the actions in the otherwise clause with your unique actions . If you try this out and have any questions, please let me know.
That's been my observation, although I've heard a pop rather than a beep. The macro above includes actions to mute all alert sounds for that brief period.