Windows are minimized when they appear

I was wondering if you could help me, when I click on a link, the new window comes up minimized in the middle of the screen, instead of being maximized like it usually does. Also to the same effect, when I used to click on a link to listen to a audio sound clip it would open a window in the upper-left hand corner of the screen, now the media player pop-ups in the middle. It seems it all started after I ran all the clean-ups on my computer and got rid of the WinnFixer Virus.

Your help is greatly appreciatted,
Ryan