I WAS experiencing this same issue. When I ran games or full screen applications that would become minimized. Eventually, after some investigation I found that it was indeed skype causing this issue...
However, this can be resolved:
The solution is simple, and will work for all versions of vista... In SKYPE, go to TOOLS>OPTIONS>GENERAL - and change the 'Visual style of the window' option to 'classic windows'. This should resolve your issue, worked for me.
As an extra measure, I also ensured that I set the windows application setting to run the program minamized. To do this, simply RIGHTCLICK THE SKYPE ICON ON YOUR DESKTOP OR START MENU > and choose PROPERTIES > and then from the RUN drop down menu, choose: minamized.