It looks like DOMXPath->evaluate()/DOMXPath->query() registers the namespace prefixes of the given context and overrides any definition from DOMXPath->registerNamespace(). PHP should not register any namespaces from the context or at least prefer manual registrations over automatic.

Reproduce code:
---------------
$dom = new DOMDocument();
$dom->loadXML(
  '<foobar><a:foo xmlns:a="urn:a">'.
  '<b:bar xmlns:b="urn:b"/></a:foo>'.
  '</foobar>'
);
$xpath = new DOMXPath($dom);

//get context node and check "a:foo"
$context = $dom->documentElement->firstChild;
var_dump($context->tagName);

// try to override the context node
$xpath->registerNamespace('a', 'urn:b');
var_dump(
  $xpath->evaluate(
    'descendant-or-self::a:*',
    $context
  )->item(0)->tagName
);

// use a prefix not used in context
$xpath->registerNamespace('prefix', 'urn:b');
var_dump(
  $xpath->evaluate(
    'descendant-or-self::prefix:*',
    $context
  )->item(0)->tagName
);

Expected result:
----------------
string(5) "a:foo"
string(5) "b:bar"
string(5) "b:bar"

Actual result:
----------------
string(5) "a:foo"
string(5) "a:foo"
string(5) "b:bar"

This bug has been fixed in SVN.

Snapshots of the sources are packaged every three hours; this change
will be in the next snapshot. You can grab the snapshot at
http://snaps.php.net/.
 
Thank you for the report, and for helping us make PHP better.

Automatic namespace registration really wasn't a good idea from the get go. 
Performance starts taking a hit the deeper in the tree a context node. The patch 
in the bug report was not used; rather a new third argument has been added to 
the query() and evalute() methods, which allows automatic registration of the 
context node to be disabled. For BC reasons auto registration is enabled by 
default. When auto registration is disabled and context nodes are used XPath 
performance will be increased.

i.e.
echo($xp->query('//prefix:root', null, false)->length . "\n");

Re-open as documentation issue:
New argument added.

This bug has been fixed in the documentation's XML sources. Since the
online and downloadable versions of the documentation need some time
to get updated, we would like to ask you to be a bit patient.

Thank you for the report, and for helping us make our documentation better.