After installing the 3.12 version of the plugin, if I create a new custom role, and try to assign capabilities to it, and I have "apply to all sites" checked, after clicking update it appears that nothing happens. I don't see any success or failure messages. If I reload the page, then none of the capabilities that were selected are checked. If I don't have "apply to all sites" checked, then the capabilities will be applied, but only to the current site.
I went back and confirmed that this was working under version 3.11. Any assistance would be greatly appreciated.