Happens on Windows 7 machine in the lab, with two monitors. The monitors has been arranged as: 2 1 and screen 2 has been selected as the primary monitor. Despite this, the start menu and the task bar is on the right monitor. When switching tlclient to full screen, the task bar is still visible and accessible. This has been verified with both 4.0.0 and 4.1.0 build3994.
This is a standard Windows misfeature that happens with all fullscreen applications, not just ours. The workaround is usually clicking the taskbar so it gets focus, then clicking tlclient so it regains focus. At that point Windows usually figures out the correct stacking order and puts the task bar behind tlclient.