The first time you run xOrganizer or xToolbox it is possible that Windows Defender or your virus scanner gives a warning, like this:
This is because these scanners search in their online databases and treat any relatively unknown applications as potentially harmful, but not because they actually found anything unusual in the code. Just tell your scanner to trust xOrganizer or xToolbox. For Windows Defender you have to select “More info” and after that “Run anyway”.
Please be assured that there is no malicious code in xOrganizer ans xToolbox (it would be really bad for business for the X-Plane.org store to sell applications with bad code). But this is why it is so important to only (buy and) use applications from trusted sources