As you've discovered, valid mark-up is not guaranteed to be cross-browser friendly. Maybe some day, but not quite yet.
At first, it sounds like you may be wrestling with a quirks mode/standards mode problem [webmasterworld.com]. If it really is just a padding issue, then declaring explicit padding numbers for the elements involved (sounds like <body> in this case) should fix it.
The peculiar part of your report is that the page renders the way you want locally but not from the server. If the server is not injecting more code, then I really don't know why that would happen. We have a lot of well-informed members here. I'm hoping one of them might chime in.