Try rebuilding a template and see if the problem persists. Some screwy things can happen with templates created in earlier versions. I was told by Steinberg that it is good to rebuild your templates with each major version change of the software.
I would try this if you can cannot create the problem using a blank project with a sole midi track. If the problem persists coming from an empty project (starting a project from scratch) I got nothing else for ya. I suppose bootcamping is in order (which I do on my macbook for live recording).