I can definitely confirm this!
Has been around since the first alpha I've tried and as of today it's still 
there.
How to reproduce:
1- configure your xserver in order to have 2 separate x screens :0.0 and :0.1 
no xinerama no twinview
2- at a first look the menu load correctly and you have two gnome panels as 
expected one per monitor
3- try launching an app it opens on the first monitor :0.0 even if launched 
from :0.1

the solution above works and that's how I've been working around the
issue. so it seems the enviroment variable DISPLAY isn't set correctly
causing this extreme usability bug which was not present on the previous
release of ubuntu. I hope this will be fixed soon because it hinders me
entirely from using my computer

-- 
Applications launched from the menu running on DISPAY=:0.1 are opened on 
DISPLAY=:0.0
https://bugs.launchpad.net/bugs/345595
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