By default, Polylang caches the home urls. You have to de-activate it by setting PLL_CACHE_HOME_URL to false either in wp-config.php or in (file to be created) wp-content/polylang/pll-config.php
You need the development version to make this work as the option is not available in v1.3.1.
http://downloads.wordpress.org/plugin/polylang.zip