Hmm, this sounds like the window is opening at a size that makes it so that it can't be used.
I'm assuming you are talking about browser windows and not other applications (if this is a problem that involves ALL of your applications my following advice is irrelevant).
Now, windows "remembers" the broswer window size. So sometimes if you close a window that is very small, tyhe next time you open your broiswer the window will be very small.
The secret is to open it, resize it and close it so that it is remembered.
But there is a bit of a problem with that. Actually there are a few:
1) if more than 1 window is open it does not work.
2) The maximize button does not do the trick.
So try this (once again, these instructions are for browser size on opening problems, if this is not the problem it won't help. But it also won't hurt):
1) open the brower (with no other browser open).
2) DRAG the broswer window to a larger size. Do not use the maximize option. Drag the borders until it is a good size. If you would like, you can use this code in your URL bar to size the window to a specific resolution:
Code:javascript:resizeTo(800,600)
Then close the window. When you open it again the size you dragged to (or used the script to resize to) will be "remembered" by windows.
It's not always easy, so it might take a few tries.
Lemme know if it works.