I was using version 2.0.9 of the plugin but even after updating to 2.1.1 the counter isn't showing up when I select the "Facebook Like - Button + side counter" setting. It had been working fine up until a week or two ago when the counter just disappeared (maybe after a plugin update but I don't remember). If I switch to the top counter, that seems to show up fine.
Looking at the HTML output of the plugin, it looks like the counter is being output in the HTML, but for some reason it is still being given the hidden_elem class which sets it to display: none in the plugin's CSS.
<td class="connect_widget_button_count_excluding"> <table cellspacing="0" cellpadding="0" class="uiGrid"> <tbody> <tr><td> <div class="connect_widget_button_count_nub hidden_elem"> <s></s><i></i> </div> </td><td> <div class="connect_widget_button_count_count hidden_elem">0</div> </td></tr> </tbody></table></td>