I file field cannot be given a value. The value of the file field comes from the client machine, for security reasons, you cannot specify the value of a file field.
I am sending an updated copy of the WA_Cookies/Cookies.js file that should fix the problem with password fields. Please note that storing the password in a client side cookie is a security risk, client side cookies can easily be hacked and the password retrieved.
As for select lists, I have not run into an issue, can you post a link to an example displaying the problem so I can investigate?