Edit: As I wrote this I had this dreaded feeling that my "instructions followed to the letter" claim would somehow turn out to be untrue. My instincts were right. I added subscriptions.php to wp-admin and, can you believe it, it worked!
Ignore what follows!
I've installed the Subscribe by Email plugin and activated it on a test sub-blog as per the instructions (to the letter Sue ). When I click Subscriptions/subscriptions I get a Page Not Found. Subscriptions/settings displays as expected but the Save Changes button returns a 404.