Hi fmfame,
The root conflict of JomSocial with our templates (or even with Joomla default templates) is because JomSocial load their own modified bootstrap version.
You can check this conflict on Protostar template but need to modify a bit.
Open templatesprotostarindex.php and replace
<nav class="navigation" role="navigation">
<jdoc:include type="modules" name="position-1" style="none" />
</nav>
<nav class="navigation" role="navigation">
<div class="navbar">
<div class="navbar-inner">
<div class="container">
<button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<div class="nav-collapse collapse">
<jdoc:include type="modules" name="position-1" style="none" />
</div>
</div>
</div>
</div>
</nav>
This modification just enable Bootstrap navar collapse function on Protostar template.
Bootstrap use many global events (bind to document) so that when we load two bootstrap library, these events will be duplicated.
As T3 also use a vanilla, untouched version of Bootstrap, we have the same conflict with JomSocial. We do not want to apply any fix because we will need to add additional script which may not be required for other users and also may cause unexpected result.
As we are moving to Bootstrap 3, the new off-canvas will help to reduce the conflict.
But other issue may arise also. We will try to release an compatible less/javascript if needed.
Its best to ask in JomSocial forums too about this issue.
Regards