I finally figured out why I was having problems specifying sub-folders (other than trunk) in my ccnet.config SVN source control provider trunkUrl element.  After toying around with svn log (which is what CC.NET uses to find changes), I discovered it only worked on some of the folders in our repository.  As it turns out you must specify the folder ensuring you are respecting letter case.

This does not work: svn log http://mysvnserver/svn/gp/trunk/commons

This does work: svn log http://mysvnserver/svn/gp/trunk/Commons

Notice the upper case C on the second line.  I'm sure this is probably documented somewhere in the SVN docs, but I don't remember seeing it.  The other possibility is that Apache is causing the problem.  Perhaps on Monday I'll care enough to look at the docs.