"All is not lost" vs "Not all is lost"

There's a difference between:

"All is not lost" and "Not all is lost".

Many people use the former while meaning the latter. The former means that everything is hunky-dory, and all is good. Another way to phrase it would be "nothing is lost". 

The second phrase is what most people mean. It implies that losses are there, but there still is hope. Another way of putting it would be "There remains a bastion of hope".

Note: "All is not lost" could be interpreted to mean something like "Not all is lost" but it sounds clunky and vague in terms of meaning. Also the speech emphasis would be on the "All", which sounds terrible and is never pronounced that way. Usually it's pronounced with emphasis on the "not", which implies the meaning from the second phrase. You can easily emphasise either the "Not" or the "all" in the second phrase while retaining the meaning.