In the last couple of versions the upgrade size has grown so that we can update every file on the system in preperation for binary diff updates. If you cannot upgrade manually you may need to issue these commands from a SSH session or from the console:
cd /usr/local/lib && fetch http://www.pfsense.com/phpfix/php.ini
cd /usr/local/etc && fetch http://www.pfsense.com/phpfix/php.ini
This will update the maximum file post size to allow future “large” upgrades.