I'm using Tera Term, a Windows virtual terminal emulator with Wine due to a legacy application. Everything else works wonderfully, but for some reason the window requires two clicks to gain focus. After being minimized it at first comes to the foreground and only becomes focused when its "tab" is pressed again on the lower panel.
On Linux I cannot use some keys such as F1-F12 without specifying another terminal manually during login, this extra hassle is not justifiable for the end-user. With TeraTerm it seems to work out of the box.
I did not actually install the software in the usuaul sense - I just ran the executable that I copied from a Windows installation and it worked just fine besides the focus issue. I'm not actually using Ubuntu, but a modified version of it called Estobuntu which comes with some additional Estoninan software.
I have come up with a temporary solution, but it is still a bit inconvenient by setting the gnome windows to gain focus on mouse over movement.