When i use the "//regen" commands from the newest worldedit on the newest version of cleanroomgenerator, a massive hole in the world appears.
What version of Bukkit are you running? I've just tried the command and not had any issues.
Another option is that you could have a plugin that is conflicting with your world manager (I'm assuming you use Multiverse-Core) that's loading the world before Multiverse is, and thus without specifying the WGEN parameters.
Try defining the generator in your bukkit.yml file and restart your server to see if that helps and let me know how it goes.