Some of the things are a bit nit-picky and normally wouldn't be a big deal. However, each of the little things that were done to make the main style work limit what can be done with the redesign. If this were just a random site on the web, I wouldn't have said anything, but this is markup for a CSS contest. You're actively trying to get the world's top designers to look at this markup, it should be perfect.
Having | after each nav item normally isn't a big deal, but now I'm forced to have that in any restyle design I do. It should have been a border, but since it's actual "content" I can't do anything with it. Same goes for <br /> tags and inline-styles. They wouldn't be a big deal normally, but when other designers are trying to work with the same markup, it limits our ability to change it from the originally intended design.
Some of the issues jsut show that there was no understanding of how tags should be used. The entire footer is wrapped in an h3 tag, which is not only semantically dumb, but also unessecary because the footer is already wrapped in a div.
I really hate being a jerk about this, and I doubt I have any chance of winning after making a big deal about the markup, but it just seems like slap in the face when I'm trying to prove that Microsoft and ASP.NET are standards friendly when stuff like this happens. For many designers, this will be the first/only time they've worked with something from Microsoft and it just looks bad to have mistakes in the markup.