_WIN32 is supposed to be defined in 64bits, so the check "|| defined(_WIN64)" is redundant.
You probably have Slicer_BUILD_WIN32_CONSOLE ON (which is good, only the packaging machines have it OFF) so it means you are meant to have the FDMessageHandler activated.
Not sure what's the crash is caused by though.

Ideally Q_OS_WIN32 should be used.
See http://doc.qt.nokia.com/4.7-snapshot/qtglobal.html#Q_OS_WIN32

Here is the code involved.

void ctkFDHandler::init()
{
#ifdef Q_OS_WIN32
int status = _pipe(this->Pipe, 65536, _O_TEXT);
#else
int status = pipe(this->Pipe);
#endif
if (status != 0)
{
qCritical().nospace() << "ctkFDHandler - Failed to create pipe !";
return;
}
this->RedirectionFile.open(this->Pipe[0], QIODevice::ReadOnly); // <<<<<< LINE 81
this->RedirectionStream = new QTextStream(&this->RedirectionFile);
this->Initialized = true;
}

Some relevant documentation:

_pipe(): http://msdn.microsoft.com/en-us/library/edze9h7e%28v=vs.80%29.aspx

RedirectionFile being a QFile: http://doc.qt.nokia.com/4.7-snapshot/qfile.html#open-5

What about running the corresponding CTK test ?

Steve, do you have the crash in debug mode ? I don't have the problem in Debug nor Release (visual studio 2008 x64).
Do you build with some special flags ? Slicer_BUILD_WIN32_CONSOLE

This was tracked down to building a release or relwithdebinfo slicer against a debug build of qt.

TODO: isn't there a way we can detect this in CMake?

This is doable.

Since Visual is a multi-configuration IDE, this has to be done at build time when the build type is known with the help of a custom_command.