I have the simplest Java application that just works if executed from command line. But if I want to debug it through IntelliJ IDEA 14 Ultimate, the System.in.read()
It's working fine on my windows 7 machine with IntelliJ IDEA 14 community edition.
It is has been a known bug in Intellij Idea: bug description
EDIT: Apparently, as pointed out in the comments, it has been fixed since this answer was given and patched Intellij will be released in Summer 2017.