Today I got the memo from Apple as probably every other Apple developer about potentially infected Xcode installations. (https://developer.apple.com/news/?id=09222015a)
The false positive validation issue appears to be caused by containing previous iOS SDKs in order to be backwards compatible.
A clean install will completely wipe the SDK directories. When you run the validation test after a clean install it will pass. Once you copy previous iOS versions, which, for us, is iOS 8 for iPhone, the validation will fail.
This scenario was tested after updating to XCode 7.0.1 (7A1001) which was released earlier this afternoon.
In order to avoid a clean install, you can temporarily remove the previous SDK version from their respective location, and run the validation. Then, once the validation passes, copy the files back where they belong.