cant click on some desktop items

i like to reboot my laptop daily and upoin vista login i notice i cant click
on some of my desktop programs. it isnt every reboot but on occasion. also
notice that if i run a program or visit a website with buttons that i need to
click to progess it wont let me and will make the program the non primary.
what i mean is say you have internet explorer and say windows media player up
one is the primary or foreground program and the other the background one.
when i try and click a button it makes the program as if it is the background
one and buttons are non accesible and i must use the tab and arrows keys to
get to what i wish to click on and enter to act as the mouse button to click.
ive never had this issue in xp so am clueless for what to due. sorry if
wording is a bit confusing but less you actually see it it is rather tough to
explain, any help is appreciated.