The conventional structure of a Subversion repository is this:
Root
Branches
Tags
Trunk
If you're using CC.Net and you configure tagging, CC.Net creates a Tag in Subversion after every successful build. If you check out from the Root, you'll potentially see hundreds of "copies" of the code tree for each CC.Net build. Add in any possible code branches in the Branches folder, and you got a lot of code. For that reason alone, check out and update from the Trunk folder, not the Root.
Secondly, you will hit merge conflicts more often early in the project, especially with project files. Messing with the raw csproj file is messy. I've found that the easiest way to resolve a project file conflict is to:
1.) "Revert" and use the master copy from Subversion
2.) Go add the missing files back to the project