We have an rather ugly and hard to use Trac, you can report bugs and request features there:
http://trac.miranda-ng.org/newticketThough you'll have to register first^^
Otherwise, the forums also work
edit:
I can also confirm this bug with the latest dev build. (not sure if the build from yesterday had it, I didn't know how to reproduce)
The duplication occurs when the menu is opened / created the 2nd time. So just open it 2 times in the chat log or by clicking a user, and you'll have all items twice... I've only tested IRC though...
The tray icon seemed to work for me