I can not reproduce this with 2.0.0rc5-dev. I made a .htaccess with:

php_value auto_prepend_file prepend.php
php_value xdebug.profiler_enable 1

and two files:
prepend.php:

<?php
strlen("prepend");
echo "prepend
\n";
?>

index.php:

<?php
strlen("index");
echo "index.php\n";
?>

The generated profile correctly shows two calls to strlen() and the "source" file shows both prepend.php and index.php (the latter inlined).

And no feedback, because the given email address is a one-shot address.