Problem is you seem to be absolute positioning something that probably shouldn't be, and positioning it by % with a fixed width.
left:4%; for example -- 4% of 1024 is 40.96 (most browsers will round to 41). 4% of 1280 is 51.2, so naturally a different size display is going to return different results -- that's why you shouldn't absolute position major content elements in the first place.
Though telling you how to accomplish whatever it is you are doing is difficult without the content; since one shouldn't even be making layout until all of your content (or a reasonable facsimile) is marked up semantically. Just as one should NOT fix the height of any containers that are likely to have text content inside them... hence that 600px height on the first DIV and 89% height on the second one both being bad practice that will likely lead you into making a broken layout.
Not that the 1000px fixed width is a good thing either, since that's too big for even 1024 displays, and will end up a crappy little stripe for many modern desktop users.