I have the same problem, but with a twist.
I have a harmless .exe that when executed:
- with DeepScreen enabled, it gets analyzed and quarantined as malware,
- with DeepScreen disables, the app gets analyzed by DeepScreen anyway, but no malware is detected.
It started happening in RC2 (2014.9.0.2004), worked correctly in RC1 (2014.9.0.2003). Clean install didn't help.
PS. I'm using Windows 8.1 Pro (x64) (RTM/final - got it from DreamSpark).