Having the exact same issue too. When the first invoice is generated, the pay now link goes to: https://domain.com/client/pay/method/etc... when it should be https://domain.com/manage/client/pay/method/etc
This ONLY happens with the first auto generated invoice. If I go to the client's invoice and manually hit the resend button, that generated email has a link that works properly.
I've applied the rewrite rule in .htaccess as per John's suggestion, and that's working, but it still doesn't explain the problem...