I'm using that same exact Gargoyles layout from Ruthsarian for a website that I'm working on. Unfortunately, I don't have the website uploaded anywhere that you can take a look at it, but I will do so as soon as possible. I'll have it available for everybody to see when we launch the site in another few weeks (hosted at LP, of course).
I've had the same problem with other css templates: Some of them work in FF/Mz, but not IE, and vice versa. In your case, the size of your logo at the top left hand side may be the problem. That's just a guess, though. It's really not very noticeable.
There's a book out called "Teach Yourself CSS in 24 Hours", by Kynn Bartlett. I highly recommend this book if you're just getting started out in CSS. And especially if you're adapting other style sheets. You'll find that you're able to have a lot more control over what you're able to do with the layout.
BTW, I like your color scheme and what you're doing with the layout. Keep working with it, don't be afraid to experiment and find out what does and doesn't work.