Joomla version? CB version? GJ version? Module version? What exact mode did you set the module to? Your first usage of comma separation should have worked.
You exclude groups from the Groups settings. This only works with the following modes "Wall Posts, Scheduled Events, Uploaded Photos, Published Videos, and Uploaded Files modes.".
Items exclude works for the following modes "Latest Categories, Popular Categories, Latest Groups, Popular Groups, My Categoris, My Groups, Joined Groups, Wall Posts, Scheduled Events, Uploaded Photos, Published Videos, and Uploaded Files modes.".
Most likely you'll want to be using the Items exclude and supply a comma separated list of group ids there.