This is not criticism just an observation as I am debating on what to do to the layout for my site.
Doesn't having links in both the header and the menubar for the following seem a bit redundant?

• 
  
• Forums/Main Index
  
• Search/Search Box in IIP
  
• Entrance/Home
  

I did notice that here at ThreadsDev the link for Entrance has been removed. How can I do that? Also is "Mark All Read" a beta function?

You can edit the links in the ubbt_unregisterednav.tmpl and ubbt_registerednav.tmpl files.

Mark All Read is a hack... but will be standard in 6.2.