I just took a quick look at this, and it seems that the globally ignored gems list logic isn't even integrated with that text box; only through the actual settings file itself. I guess since the plugin was written, this has gone unnoticed.
You should be able to tinker with the actual settings file or the code itself for now to add in gems to ignore. I'll try to check into fixing this soonish (it's somewhat low priority at the moment), but I'm just acknowledging it is a problem.