After trying out whatever tips and tricks that others have suggested, and this issue still doesn't resolve, this maybe a permission issue; that's why things might running as root.
And no -- it's not less permissions, it maybe related to MORE permissions -- for certain files, the group or others executable permission bits might have been set. To fix this --
find <gem paths> -type f -perm -u=x -exec chmod g+x,o+x {} +
find <gem paths> -type f -perm -u=rx -exec chmod g+rx,o+rx {} +
Of course if you're planning to use the gems system wide, all files and directories must be readable --
find <gem path> -type f -exec chmod o+r,g+r {} +; find <gem path> -type d -exec chmod o+rx,g+rx {} +