They should have version numbers to identify them. What I believe is happening is that you are mistaking version 1.9.x for version 3.3.3.0 they are in two different directories. Unless you have a compelling reason to keep the older version, your best bet is to get rid of it. Different beta versions and the current version should not make a difference. The beta versions did not have any licensing code in them (you could NOT license them). The beta versions had a shut off date built into them. A simple add/remove programs built into Windows would remove the older version before you would install the newer version (as the beta versions told you about). But, the Revo Uninstaller approach is the remove it all, including registry entries for the program, just to be absolutely certain the program is gone. You will want to reinstall the latest version if you wish to continue using Scrivener. If you made changes to the Scrivener Preferences, you will probably want to save those before doing the tactical nuke option using Revo.
Sadly, Scrivener support covers just Scrivener. Basic OS support should be covered by Microsoft. Good luck getting that. Getting help for Adding and removing programs is Microsoft support. Getting a developer to spend the time with you on basic OS support is like trying to get Einstein to help you with basic math. Probably isn’t going to happen.
It’s not because of the duplicate registry entries (but they can be removed by a decent 3rd party uninstaller). It’s more likely a wifi glitch, an antivirus ACTING like a virus as they often do, or a problem at Paddle, the license server. Some people have found that the license info at Paddle was corrupted. For license issues, you need to open a support ticket.