Right now, it looks like version 3.1.3 of the plugin cannot work for a multisite setup using WordPress 3.x (I'm using 3.0.5).
The plugin's multisite-handling code makes two mistakes:
It assumes that there's a simple API for setting the network-wide settings just as easily as it's done for the per-blog options. That API doesn't exist (yet). See http://wordpress.stackexchange.com/questions/18314/global-settings-page-for-multisite-plugin. The current code writes to the per-blog settings and then tries to read the network-wide settings. So now you know why saved keys (and other settings) will not be read back.
It tries to set/read all settings, whether network-wide or per-blog, using a single method (which as I described in the previous bullet point is broken). The plugin should use two separate methods depending on which settings page the admin is using: (a) read/write network-wide settings manually and (b) read/write per-bog settings using Settings API.
Right now, it looks like version 3.1.3 of the plugin cannot work for a multisite setup using WordPress 3.x (I'm using 3.0.5).
The plugin's multisite-handling code makes two mistakes:
I've included a workaround at: http://wordpress.org/support/topic/doesnt-save-keys-for-wordpress-305