Are you using the 'Gold Cart for WP e-Commerce' paid-for extension to WP e-Commerce?
If so, you will need to move the PayFast files to a different location to have PayFast appear as a payment method.
Move the individual PayFast module files from:
wp-content/plugins/wp-e-commerce/merchants
to:
wp-content/plugins/gold_cart_files_plugin/merchants
in your installation. This will resolve your issue and PayFast will then appear as a payment method within Gold Cart for WP e-Commerce.