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 TOOLSOPTIONSGENERAL - 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.


--
thomasbill