That's because SimpleXML doesn't understand Atom's way of mixing content.  The first summary node, for example, looks like this:

<summary type='xhtml'><div xmlns='http://www.w3.org/1999/xhtml'>Last Monday, we spent some time at the <a href='http://www.u-tokyo.ac.jp/index_e.html'>University of Tokyo</a>, where we talked about Ruby and so on; quite a change of pace from the rest of the visit.</div></summary>

That means that there isn't actually any string value in the summary node.  There is however a div node there and that div node has string contents.  Normally you would either encode the HTML or use a CDATA block there which is probably what you had when you refer to it working before "with nested tags".  SimpleXML has no idea that <div> is an HTML element and not an XML element.  How would it?

So you can get the string like this:

(string)$x->entry->summary->div

But note that inside that div element, you have an <a href> element.  The easy way to see the structure is to just do this:

print_r($x->entry->summary);

Which gives you this:

SimpleXMLElement Object
(
    [@attributes] => Array
        (
            [type] => xhtml
        )

    [div] => Last Monday, we spent some time at the , where we talked about Ruby and so on; quite a change of pace from the rest of the visit.
)

And print_r($x->entry->summary->div); which gives you:

SimpleXMLElement Object
(
    [a] => University of Tokyo
)

You need to apply some Atom-specific logic in order to use SimpleXML to parse an Atom feed.  One trick would be to do:

echo $x->entry->summary->asXML();

which gives you:

<summary type="xhtml"><div xmlns="http://www.w3.org/1999/xhtml">Last Monday, we spent some time at the <a href="http://www.u-tokyo.ac.jp/index_e.html">University of Tokyo</a>, where we talked about Ruby and so on; quite a change of pace from the rest of the visit.</div></summary>

You may not want the summary element itself.  You could avoid it by doing something like:

foreach($x->entry->summary->children() as $child) echo $child->asXML();

But basically there is absolutely nothing wrong with SimpleXML here.