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I'm having the same problem, I posted a thread asking about it yesterday. I even get similar looking broken tags at the bottom of the forum.
I'm also using a custom theme for my site. I laid out the theme for the forums on a mirror site; basically I did a second install of xoops, put in Newbb 2.0, and altered the templates to where I wanted them.
Then, when I went back to my main site and did the upgrade, the problems occurred. I never actually put the custom template files onto the main site; since the forums weren't working with their base files, I didn't think uploading my new ones would help matters any.
Anyone know what's going on here? As far as I can tell, this was just an upgrade bug; doing a new install, adding my custome theme, and then installing NewBB everything worked fine.