Vjcobra & David. Thank you for bringing this to my attention.
If you have CleanSync enabled; the offending cleaning rule will automatically be removed the next time you run System Ninja.
If you prefer manual removal, the cleaning rule is located at %programfiles%\System Ninja\scripts\microsoftnet.ninjascript
Apologies for any trouble. If anyone needs help repairing their .NET install, feel free to email me from the contact page.