Hi Jonesey,
Seems to work OK here...two instances of Rapture, some MIDI data on their tracks and switching through screensets without a problem.
Win 8.1 x64, Sonar 64-bit X3c, 64 bit engine on.
Ya know, I seem to recall occasionally having problems after updating with projects or templates that were created in older versions. Did this problem creep up after updating? If so, does it persist when you create a new project from scratch?
Dean