Welcome to the wonderful world of web design...
CSS is great, as far as it goes, but many of the things that should work in a certain way often don't, and you usually find you have to write browser-specific hacks to get even relatively simple layouts to display properly in IE and Firefox.
Here's a link to a really nice and relatively simple three column layout with header: click here
The centre content area is fluid while the left and right panels are fixed width.
Here is another example that really deserves some attention: click here
I imagine your columns (left/right/main content) are conflicting with how the browser interprets the page.
I get a bit vexed with browsers - the software often seems to let down web code standards that should work but that ends up by being misinterpreted, so we still need browser hacks...