As it happens, I have been using my Ubuntu desktop with a Mac OSX-like theme with these menus on the left-hand side for many years. I draw this to their attention because as from version 10.04 (Lucid Lynx) of Ubuntu the out-of-the-box settings for placement of these icons now matches mine.
At the tine of writing, not only does the iPlayer place these icons in the wrong place, but they use their own artwork for these icons too. FOR THE LOVE OF GOD, WHY? Please trust the operating system to do the job and don't presume that you know better. Because you don't.
This is what they should be doing on my system: (Tweetdeck another Adobe AIR application)
This is what they are doing:
Of the countless applications I have used, this is the only one that I have encountered that knows better than the window manager and puts the system menu buttons in the wrong place (for me).
Please, please fix this before you release this version into the wild as a little part of me dies every time I try to minimize your application.