Without an expire in the future you have a session cookie, i.e. it will expire when the browser closes. Appears that Netscape considers new windows to be part of the session, where IE is not. Are you opening new windows from within the open browser ( file->new ) or are you starting it up from an icon on a desktop? Seems a new window via file->new would be considered part of a session, while new windows from icons would be a separate instance, thus separate session.

Using CGI.pm to at least generate the cookie would provide you with an easy method of creating a properly formatted expires= string. good luck!