What's in the folder? Could it be the installer/updater that you downloaded? If so, I'd keep it just in case I have to reinstall or my computer dies and i need to install on a new machine.
Can't think of any other reason why you'd get a new folder on your desktop.
Same thing happened to me. I have a 'v3' folder and a 'v4' folder. Both are basically identical--a bunch of PDF files in different languages, and a setup application. Can/should I delete 'v3'?
Sounds like all your installer files--probably the decompressed files generated during the installl, though I'd except to see them in the temporary folder instead of your desktop.
I know of no reason to keep the v3 so long as you keep backed up copies of the v4 installer.