I haven't used Subversion, but there are similarities with all source code control products. I'm guessing you have some sort of client specification that maps your SCC depot structure to directories on disk. Since the physical directory structures of Windows Vista differ from Window XP, you already need to account for this in your SCC setup (e.g., different client specifications per machine). My guess is that you'd still need to account for these differences with the new directory structure since the actual physical directory path of Public Preferences differs between Windows Vista and Windows XP. Is that OK?
Also, keep in mind that there might be multiple directories to sync from your Subversion depot -- such as Public Preferences and possibly Public Documents, depending on how many files your group shares.
It's fine to have different folders in XP and Vista. I could care less. I can pick the folders manually if the LabVIEW documentation is reasonably clear. My point was that I want to clone my setup into one or two folders, rather than having the configuration spider into dozens of different folders and registry entries, making it so complex that I can't clone my environment without writing a big software application to do it for me. Thanks.