Hey Paul. I was getting the beep too. It's coming from Windows. I actually turned it off on my system and then forgot about it. I'm not sure what I can do about it, I'll have to check. In the meantime, unless you actually want it, you can shut it off by going to Sounds portion of the Control Panel. Go to the Sounds tab in the Change System Sounds. I believe it's called "Default Beep", or something like that. Just set it to "none".
As for the taskbar issue, I see that one too. AutoHotKey scripts show up in the lower right portion of the taskbar as a green box with an "H" in it. (you might have to hit the up-arrow to see it among the other running tasks). Again, not sure how to deal with that, but you can easily bring the keyboard back on top by typing the win->space key combination twice to hide it and re-open it. It will pop back up on top.
I'll try to look into better solutions, but that may not happen right away. In the meantime, see if these suggestions aren't a help.
Thanks....