This was reported by Sven Lafebre <s.lafebre@runbox.com> :
I noticed that the flag MITK_SHOW_CONSOLE_WINDOW is not honored when using the mitk_create_executable function. I created a patch for the latest 2018-04 release branch (ba4a121c0b) that solves that issue and also adds support for Windows .rc resource files.
Proposed patch by Sven: