I'm not 100% sure why Mathematica is launching with the oversized window.
However when I have windows that go off screen and I want to move them so that you can see their title bars you can hold down the ALT key and then put the mouse anywhere on the window you want to move, and then hold down the left mouse button and drag the window in place so that you can see the title bar.
Example

NOTE: In the above screenshot you can see that when you press the ALT key that the cursor changes to a hand (in GNOME). When this happens you can then move the window as if you had selected it by its title bar.
Can I change the size?
I found this question asked on the Mathematica SE site titled: Opening new notebooks with a non-default window size which mentions that you can change the size of the notebooks when they open up as follows:
excerpt
The default window size can be controlled from two different places. The first is the Global $FrontEnd WindowSize
, set through the Option Inspector → Global Preferences or with:
SetOptions[$FrontEnd, WindowSize -> {300, 900}]
The second is the WindowSize
of the style sheet itself. If it is defined, the WindowSize
of the style sheet will overrule the setting above. You set the style sheet size through the Option Inspector → Selected Notebook or by evaluating this inside the style sheet itself:
SetOptions[EvaluationNotebook[], WindowSize -> {300, 900}]