I confirm the glitch - after switching desktops the program is minimized into a small window in the upper left corner. Moreover, on my system (SuSE 9.3) only few buttons are visible, the rest are just white. The mousover works so it is really just an annoyance, not a real hurdle. No other issues detected yet. The screenshots of both issues are at http://www.asmirnov.org/misc/chemsketch