I run Mathematica 8 on a Linux machine. I have recently switched from using openbox as my window manager to a tiled window manager called i3wm. Mathematica was sort-of usable in openbox, but doesn't play nice with i3wm. In particular, the Documentation Center is completely non-functional. When I try to use it I get a zombie window that permeates all workspaces and cannot be killed, necessitating a hard restart of X or a system reboot. I have not noticed a similar problem with any software (other than Mathematica) that I have used on this system, including Eclipse, Netbeans, Chromium, etc.
So why doesn't Mathematica interact with Linux window managers in a standard manner? As of now, Mathematica is basically unusable on my system. I had noticed some Mathematica UI ``quirks'' in openbox, and also in Ubuntu's Unity, but nothing compared to this... It seems the UI is basically a hack... very disappointing. Is there any plan at Wolfram to make Mathematica functional on Linux systems? It seems like Wolfram has shipped an unfinished, untested product.