Comment 2 for bug 1000469

I have a similar problem, but not just update-manager. TeXMaker also starts in a "maximized size", but offset to account for the unity launcher and top bar. It may also be some other programs, but that's the one I use the most so I can't confirm if thats an exhaustive list.

In 11.10, the programs opened maximized everytime, no problems.

(12.04 64-bit, Dell XPS17, nvidia x/swat)