I can reproduce this.
I'm building my self on Arch linux using gnome-shell and qt 4.8.4. To fix it I can just change the geometry in GoldenCheetah.conf to something smaller than the screen.
To reproduce I switch it to full screen, then close GC. It seems to work every time.
I put break points in QTFullScreen. Basically when it loads it doesn't know that it's full screen (isFull == false), I think the title bar is being drawn off screen. There's no good way to grab and move on Gnome-shell. I think perhaps when changing from full screen GC should check it's geometry and if it is the same size as the screen or larger, it should resize to something more sensible. I can't think of a slick cross platform way to do this.
When maximised but not full screen I have (0 52 1366 716), when full screen I have (0 0 1366 768).