I am a new Cubase user, and I was seeing the same behavior in Cubase Pro 8. Like johnstaf, I was able to solve it by merging my two streams (in my case my keyboard and a breath controller) in MIDI-OX then getting it into Cubase using the LoopBe1 Virtual MIDI Driver.
Is it me or is it a little ridiculous that this $550 program requires the use of two FreeWare band-aids in order to work right?