I have wp 3.2.1
and just upgraded Ata from 3.6.4 to 3.7. 1

I have created a widget area with 5 cells and each cells have 2/3 text widgets in the footer. I had applied top bottom padding (css inserts) to these text widgets which worked perfectly in version 3.6.4. But after upgrading this is lost.
I tried many combinations (with the help of firebug) but nothing seems to work. on my test site here too it is not working. feeling so stupid. Please help.

what is the exact code you used to create the widget area?

go to ATO->export/import settings and export your settings and attach them to a reply

here is the exact code
<?php bfa_widget_area('name=ft&cells=5&align=8&align_2=1 &align_3=7&align_4=2&align_5=3&before_widget=<d iv id="%1$s" class="header-widget %2$s">&after_widget=</div>'); ?> (copied from ata options)

and otherwise in the attachment the way you want.
Thanks

something weird is happening at your site. When I look at the footer I see

<td id="footer" colspan="3">
    <p>
    <table id="ft" class="bfa_widget_area" style="table-layout:fixed;width:100%" cellpadding="0" cellspacing="0" border="0"><tr>
<td id="ft_1" align="left" valign="middle"></td>
<td id="ft_2" align="center" valign="middle"></td>
<td id="ft_3" align="left" valign="bottom"></td>
<td id="ft_4" align="center" valign="top">
   <div id=\"meta-5\" class=\"header-widget widget_meta\">
     <div class="widget-title"><h3>Meta</h3></div>			
       <ul>
	<li><a href="http://tp.design-flute.com/wp-login.php">Log in</a></li>
        <li><a href="http://tp.design-flute.com/?feed=rss2" title="Syndicate this site using RSS 2.0">Entries <abbr title="Really Simple Syndication">RSS</abbr></a></li>
	<li><a href="http://tp.design-flute.com/?feed=comments-rss2" title="The latest comments to all posts in RSS">Comments <abbr title="Really Simple Syndication">RSS</abbr></a></li>
	<li><a href="http://wordpress.org/" title="Powered by WordPress, state-of-the-art semantic personal publishing platform.">WordPress.org</a></li>
		</ul>
</div><div id=\"text-12\" class=\"header-widget widget_text\">			<div class="textwidget">passing</div>
		</div><div id=\"text-11\" class=\"header-widget widget_text\">			<div class="textwidget">charming</div>
		</div>
</td>
<td id="ft_5" align="right" valign="top">
</td>
</tr></table>

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    </td>

notice the lines with the backslash (\)? that shouldn't be there

Try this, deactivate all your plugins and see if things start working them.

OMG.
but there was only one plugin and only active (jetpack) that i deactivated immediately. Nothing happened.
But saw a drop-in (install.php) which I know I had not put. (immediately logged on to my cpanel and deleted that drop-in).
worried more now.
I saw the slashes but thought may be it in in upgrade?!!

Going to check my main site's footer

if you want me to take a look, send me a PM with an admin ID/pw and I'll peek

Oh this means a lot to me! Thankx.

I just checked on my main site these weird slashes are there too. Am at the moment deactivating plugins and checking. If prob not solved will get back to you. (probably tomorrow)

entered twice so removed this post.

It works perfectly in 3.6.4 but not in 3. 6.9 Ata Version.

the funny thing is I have put another widget with simplest Code in the footer:

<?php bfa_widget_area('name=My new widget area'); ?>
(without cells)
then it works and is without weird slashes

the backslash's in the code are caused by the PHP option 'magic_quotes_gpc' being set to 'on'.
you need to edit the php.ini and add

magic_quotes_gpc = off