Yes of course you're right it's crappy, but except this one it's just perfect for my needs.
Unfortunately the developer has stopped developing it and only accepts patches now.. its written in python, so if you know what you're looking for it should be simple to fix.
Well, the problem seems to be even more minor from what i noticed just now:
In pypanel, in the right hand are where is the icon tray. there is no amsn icon, but, the 'area' that the icon should be is occupied.
If you click on the empty space, amsn shows up, if you click again it hides, right click works etc. Just the icon is not visible anywhere.
I haven't noticed it before because there was no empty space between to other icons..
Here is a screenshot of the bottom right corner of the desktop running pypanel, I think it's pretty obvious:
If functions like there was an icon there, but there is not