I'm not exactly sure what a 404 error is. I know that if a URL has been deleted you will get one. Currently my forum is showing (43) 404 errors in Webmaster Tools.
About (10) of them I understand. They are posts that have been deleted.
I think you are talking about the URLs found in our script code (I mean those that don't contain PostLink.jtp). The problem is that googlebot tries to parse our javascript code and fails. This is a problem that google should fix. I may research this soon, but this shouldn't harm your pages and SEO.