See if this helps:

http://www.ijoomla.com/option,com_smf/Itemid,6000/topic,387.0/

Though it doesn't really talk about indentation, but with my experience with the program you need to make sure that you don't have pictures only for the first item set or intro for the first item.  Make sure everything is uniform when it comes to article presentation.

You might want to try going into the layout manager and hilighting the item with the indent, then with your editor just click the left align button.  I know that the news portal automatically sets up the vertical alignment to center so I have to put in html to verticle align it to the top, so it sounds like that might be the problem.

So your code should look something like this:
<td align="left" valign="top"> noting that valign is verticle alignment so you only need the first part.