Wrap the form tag around your span divs. This is working for me, but you might need to tweak things a bit:
<div class="row">
<form class="form-horizontal">
<div class="span6">
<fieldset>
<legend>Legend text</legend>
<div class="control-group">
<label class="control-label" for="input01">Text input</label>
<div class="controls">
<input type="text" class="input-xlarge" id="input01">
<p class="help-block">Supporting help text</p>
</div>
</div>
</fieldset>
</div>
<div class="span6">
<fieldset>
<legend>Legend text</legend>
<div class="control-group">
<label class="control-label" for="input01">Text input</label>
<div class="controls">
<input type="text" class="input-xlarge" id="input01">
<p class="help-block">Supporting help text</p>
</div>
</div>
</fieldset>
</div>
</form>
</div>