I've had this problem for a long, long, long time but only with one website and only in Safari. I've used cmd-\ to fill in the username/password but the extension ALWAYS asks me if I want to save the new login. I've tried saying "no", and it just happens the next time I visit the site. I've tried saying "yes" and saving over the old entry. I've tried saying "yes", creating a new entry, and then deleting the old one, etc. It just continues to happen every single time for this one website.
Oddly, going to that website from another browser like Firefox doesn't have the same problem.
It's very weird.
It sounds like your issue is different since you are already using the ⌘\ keyboard shortcut to fill the Login. I've split your post from the other thread because of this. I want to make sure you get the attention you deserve. I hope you don't mind.
What is the URL?
What happens if you simply choose the "Never autosave for this site" option to disable autosave for that specific domain?
Please let me know.