[Flash Scan after update pop-up]

I have my program scheduled to update and to perform a flash scan after update, which is working fine- except it creates a popup to show the scan in progress. This interrupts other things I am doing by blocking the screen and covering the other application I am engaged with.

Is there a way to prevent the popup, and let the flash scan run in the "background", or do I need to disble this feature to prevent the interruption?

Thanks!