[edited bug name]

Could you please provide a short reproduce script for your issue? I tried the following code, which autoloaded 'A\B\C', not 'D':

<?php
use A\B\C as D;

if (!isset($alreadyIncluded)) {
	spl_autoload_register('var_dump');
	$alreadyIncluded = true;
	include __FILE__;
} else {
	new D;
}

You are correct, the provided test file has no problems.
The error I have is with a slightly more complex setup - a composer-generated autoloader class.
I will try to reproduce the error with a minimal setup...

Here's a test file with a somewhat odd result:

<?php

use A\B\C as A;

if (!isset($alreadyIncluded)) {
    spl_autoload_register('var_dump');
    $alreadyIncluded = true;
	include __FILE__;
} else {
    class_exists( 'A' ); // 'A'
    new A; // 'A\B\C'
}

...and apparently it has nothing to do with re-including the original file (my bad)

String class names must always be fully qualified, i.e. if you need to write class_exists('A\B\C'). Namespace aliases don't work in strings.

If you are using PHP 5.5 you can alternatively write class_exists(A::class).

OK - but then maybe this could be made more clear in the docs?

The behavior of namespaces with "dynamic" features in documented in http://php.net/manual/en/language.namespaces.dynamic.php