Minimising windows and jedit not opening properly

I've just set up Ubuntu and started using it for the first time.

I was using it fine. When I minimized windows they appeared at the bottom of my screen, on the taskbar, much like a Windows computer. I was also successfully using jedit and doing some C++ programming.

Then, as far as I can tell, it randomly stopped showing what windows were minimized at the bottom of the screen. How did this happen and how do I rectify this?

That is not the most important thing, I can live with it. However, after minimizing a jedit window and losing it I find that I cannot even open a new jedit window at all (even after restarting my computer several times). I type jedit in the command prompt - I get the grey box with jedit written in it, but then no actual jedit window comes open so that I can edit code. Or, I click on the jedit icon itself and it does the same thing.
What the heck can I do?! I need to program and it's not working!