There is one simple thing that you may forget in your RealURL configuration and it will screw up your sites.
If (1) you use have than one site in the page tree and (2) you have pages with the same path in both sites (like, /news/), you need to pay attention to one small detail: do not forget to configure all domains. For example, if you configured non-"www" domain but forgot to configure "www" domain, realurl will not be able to find correct page ID from URI when user visits "www" domain. User will either get "Page not found" or page from wrong domain (technically - page from the first domain in the tree, if page with such path exists). This is unavoidable limitation of RealURL.
If this error happens, you may see entries in RealURL error log for non-existing pages and RealURL 1.1.4 and newer will complain in admin panel about missing rootpage_id.
However, if you write your configuration correctly, you do not need to worry about it all. So always check your configuration carefully.

I'm sure there is a smart reason... but I wish realurl could look it up for me... or generate config code based on sys_domain... :)
polarizers 2 cent