I have this odd problem that I cant seem to fix when I open certain windows its cut off an example can be found here.
My res is 1366x768 its as high as it will go. Any help will be most welcome
From the picture, it looks like you have your bottom panel set to be "on" all the time, yet have not set it so that it will not cover your app windows while it is on the screen. Is that what you mean? If so, configuring your panels for "auto-hide" behavior (or, if you feel that you need to have your panels on the screen at all times, to reserve space for your windows) should take care of things.
If, OtOH, you mean that your app windows are larger than your display's size and not simply fitting your screen but being covered by your panel(s)... I have experienced the occasional non-maximized window that was larger than my display. This was easy to fix by right-clicking on either the window's title bar or on the window's representation on the panel (if using the Window Buttons thing) and selecting the resize option. One can also (generally) just choose to maximize the window; it might be counter-intuitive, but if an un-maximized window is larger than your display, selecting maximize will actually shrink the window (therefore, the command is mis-named - but we appear to have taken the lazy way and taken Microsoft's name for the command to use in linux) to the size of your display.