The downloads page (http://www.scorpionsoft.com/downloads/2fa) we list "v5.0.1" as the latest version, as this is the version of the software files. That means you will see "v5.0.1" in the latest version when you are looking at an AuthAnvil 2FA webpage on your server.
"v126.96.36.199" refers specifically to our install executable, AuthAnvilTwoFactorAuth.exe. This file has a different numbering scheme because it may not be upgraded at the same pace as the core software itself.
The changes between those 2 software file versions (v188.8.131.52 to v5.0.1) are very small, as they only apply to a certification requirement with Server 2012. Since AuthAnvil is included in some of Microsoft's application catalogs we make sure our software is always up to date with the latest certification standards. This patch doesn't affect the end user performance and all of our customers running AuthAnvil on Server 2012 are still able to run at 100%. Because of this, we released it silently for any new customers downloading the product but are not requiring any existing customers to upgrade.