I'm using the latest Bootflat version (2.0.1) and Bootstrap (3.1.1) and my table font-size is 16px instead of 14px.
<html>
<head>
<link rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css">
<link href="/packages/bootflat/css/bootflat.css" rel="stylesheet" type="text/css" />
<link href="/packages/crm.css" rel="stylesheet" type="text/css" />
<link href="http://fonts.googleapis.com/css?family=Open+Sans:400,300,600,800,700,400italic,600italic,700italic,800italic,300italic" rel="stylesheet" type="text/css">
</head>
<body>
<div role="navigation" class="navbar navbar-inverse navbar-fixed-top">
<div class="container-fluid">
<div class="navbar-header">
<button data-target="#bs-example-navbar-collapse-1" data-toggle="collapse" class="navbar-toggle" type="button">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a href="#" class="navbar-brand">CRM</a>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="http://www.crm.tst/contacts">Contacten</a></li>
</ul>
</div>
</div>
</div>
<div class="container-fluid">
<div class="row">
<div class="panel panel-default">
<div class="panel-heading">Contacten</div>
<table class="table">
<thead>
<tr>
<th>#</th>
<th>First Name</th>
<th>Last Name</th>
<th>Username</th>
</tr>
</thead>
<tbody>
<tr>
<td>1</td>
<td>Mark</td>
<td>Otto</td>
<td>@mdo</td>
</tr>
<tr>
<td>2</td>
<td>Jacob</td>
<td>Thornton</td>
<td>@fat</td>
</tr>
<tr>
<td>3</td>
<td>Larry</td>
<td>the Bird</td>
<td>@twitter</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<script type="text/javascript" src="/packages/jquery-1.11.0.min.js"></script>
<script src="//netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js"></script>
</body>
</html>