No, that always used to be a problem and yes, nothing has changed. Miracles like the Cataclysm do not interfere with your free will because people can still believe it just rained a lot. On the contrary, Jesus always asked someone if he/she believed before healing them or their children from an illness, for example.
How about Joshua? When fighting the Amorites, Joshua told God to halt the Sun and the Moon. God stopped the Sun and the Moon in the sky for a whole day. How is that not God proving his existence to Joshua?
But, hell, let's not even go as far as miracles. What about Jeremiah? God not only had a conversation with him while physically present, he touched him. How is touching someone not establishing that you exist?