I am using Suffusion theme, after installing Social plugin the reply option on comments disappears.
It's there with several other themes.
It's there if I deactivate Social.
I have also deactivated all other plugins.
I don't think it is a CSS issue as the HTML for "reply" is not there.
So I am guessing it's an incompatibility between Social and Suffusion PHP. I'm not sure how best to process.
Suffusion 3.9.4 http://wordpress.org/extend/themes/suffusion
Social 2.0 http://wordpress.org/extend/plugins/social/