Some websites open windows with a specified size, and seem to override whatever settings you have made -- I know after a visit to my online banking, the windows open in different sizes.
Try this:
With ONLY ONE IE6 WINDOW OPEN, right click on a hyperlink and select OPEN LINK IN NEW WINDOW. Don't maximize the new window (assuming you can see it at all; boy I hope so). Close the original window, then resize the newly opened window to the size you want. Hopefully all of your new windows will open to that size.