As I mentioned earlier, I did have the "recursive" checkbox checked when I synchronized and got the results I posted.
I am having a hard time finding the web.config settings you describe. Is this the section?
<!-- allow large file uploads -->
<httpRuntime executionTimeout="600" maxRequestLength="8192" requestLengthDiskThreshold="8192" useFullyQualifiedRedirectUrl="true" />
Sorry - my web.config file is over 300 lines long, and it is hard to find if you don't have a unique keyword. Thanks for your continued replies.