I just ran into this issue. Here is how i have been able to fix it.
I renamed go-pear.phar to go-pear.phar.old and downloaded the go-pear.phar from the pear website:
http://pear.php.net/go-pear.phar
and I ran it as :
php go-pear.phar
And everything went fine. There is of course some issue with the one that Zend provided.