It happens when using the hardware too. What I generally have set up as a Pro Tools template is:
A click track, 2 Instrument tracks, one with Spark and one with Analog Laboratory (Or I will once I get my activation code
An audio track, 2 Aux and a Master. A reverb and a delay on the Aux sent to the Audio and Instrument tracks.
That's what i start with then the session gets bigger, but I find it happens only when I use Spark. Everything else is really stable.
PS. If you have a moment, do you mind taking a look at a few things for me, Support case 132836, also Midi in Pro Tools with Spark. I can drag Midi from the Library and It plays, I can drag in Midi from other sources and it plays. But I can't get Midi into Pro Tools by using the Spark pads. I have both of the Midi from pad and sequencer preferences set to yes in Spark.