Every time I boot up Scrivener 3 for Windows I have to reenter my licence details as I keep getting deactivated 
I would suggest uninstalling Scrivener completely. Downloading it again. Reboot for good measure. Then reinstall Scrivener, and activate it again.
I heard from one user whose licensing files at Paddle were corrupted and they had to recreate the account.
Open a support ticket with L&L directly; for privacy purposes they do not talk about licensing in the forums. If there is a problem with your account they can help you.
Reinstalling seems to be working, but I’ll keep the other ideas in mind, thank you!!!