This topic is pretty old. The old problem of receiving more than 1 upgrade notification per day / 24 hour period was fixed many BPS Pro versions ago. Unfortunately, when you do upgrade your site and the Upgrade Check Cron check fires at the same time then you will get 1 upgrade notification. You will not receive any more upgrade notifications after BPS Pro has been upgraded.
To turn off BPS Pro upgrade email notifications go to S-Monitor >>> Email Alerting & Log File Options and choose the options you want to use.