I just updated my site to XenForo 1.5.12 and there were two outdated templates that I merged with the parent version. Now the online status indicator is missing on avatars.
You probably merged incorrectly.

The top of the template should look like:
<xen:require css="message_user_info.css" />

<div class="messageUserInfo" {xen:if $user.user_id, 'itemscope="itemscope" itemtype=""'}>
<div class="messageUserBlock {xen:if $user.isOnline, online} {xen:if @xb_animated_online, 'xbOnlineAnimated', 'xbOnlineRegular'}">
   <xen:hook name="message_user_info_avatar" params="{xen:array 'user={$user}', 'isQuickReply={$isQuickReply}'}">
       <div class="avatarHolder">
           <span class="helper"><span></span></span>
           <xen:avatar user="$user" size="@xb_avatarSize" img="true" />
           <xen:if is="{$user.isOnline}"><span class="Tooltip onlineMarker" title="{xen:phrase online_now}" data-offsetX="<xen:if is=" @xb_animated_online">-10<xen:else />-22</xen:if>" data-offsetY="-8"></span></xen:if>
           <!-- slot: message_user_info_avatar -->

<xen:if is="!{$isQuickReply}">

This is updated for 1.5.12, we'll be pushing out an official update shortly.

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