First big thanks to you for your very useful plugin.
I'm using it on a multisite install too and I've got the same problem > it can't save settings through my network (when I click apply to all sites, box is checked first but when I get back to the role it's not checked/saved anymore http://screencast.com/t/zXH1jhrgP)
I've read your FAQ and tried the alternative update options through config.php but it doesn't help.
Could it be a file permissions problem? (I'm on WPengine hosting)
Thank you very much for your help!