I learned at the 12/15/09 WDN meeting that the batch validator fails when it finds a broken link. A tool to find bad links is "Xenu's Link Sleuth". The name comes from the author's strong feelings about Scientology, but that isn't relevent to the functionality of the software.
Sorry, OS-X users - it is for Windows only.
I've used it for years and I like what it does.
Give the starting point in complete form - "http://site.unl.edu/" or "http://site.unl.edu/subsite/"
Don't omit the "http://" or the final "/".
Unselect "Check external links".
Under "more options", chose as few functions as you need - I prefer "ordered by page".
When I want to find orphan pages, I select that by itself and do a new run.
If a troubled site causes time-outs use fewer threads. A clean site checks faster with more threads.
It helps to have a fast connection and a reasonably powerful computer. When I tried checking a 5,541 URL site using a Pentium 4 WinXP desktop with 1GB ram, it choked. A low-end core2 duo Win7 notebook with 4GB ram did it in 47 seconds.