There appears to be a conflict with WooCommerce. Both plugins use the taxonomy 'pending' so when WooCommerce tries to change something from 'pending' to any other order status things break.
This should be fixed with WooCommerce 2.1 - https://github.com/woothemes/woocommerce/issues/3064
I guess this is more of an FYI for other Edit Flow users rather than actually needing support. :)