I figured out the bug that was causing it to not allow style changes. The custom header template didn't have the cookie path and cookie domain values set. So it was getting an additional bbuserstyleid cookie with path of "/" along with the previous cookie with path of "/forums". This double cookie was causing the issue. I added those two lines to the header template and it works..
Although some css on the toolbar where the username, search and message link is messed up. It's all scrunched to the left and doesn't scroll.. like it has an absolute positioning.
http://screencast.com/t/q8lH8qQIqqc
http://screencast.com/t/ifi3mLgsG7