I finally figured this one out, and it was a doozy. It turned out to be an issue with my DB and not this plugin. I will go ahead and outline my fix anyway just in case someone else runs into this issue.
In the pre_options table for the main site in the network, there were entries for both pre_users_roles and wp_user_roles. wp_user_roles contained all the data and pre_user_roles was empty. I deleted pre_user_roles and renamed wp_user_roles to replace it and viola, everything worked.
Note:for this example the custom wp table prefix is pre_