You basically have 2 pear installations on your machine, and the “pear upgrade” command updates the other one, not itself.
I assume that the pear version you’re running has been installed via ubuntu’s apt.
Find out where it has been installed with apt (on Debian/Ubuntu):
$ dpkg -L php-pear
...
/usr/share/php/PEAR.php
...
/usr/bin/pear
Now let’s see where pear installs the files to:
$ pear config-get php_dir
/usr/share/php
On my machine, it is the same – but probably not on yours, which is the problem. Fix it by setting the php_dir, as well as the bin_dir:
$ pear config-set php_dir /usr/share/php
$ pear config-set bin_dir /usr/bin
Alternatively, remove the ubuntu pear and install it freshly from http://pear.php.net/go-pear.phar