I was reading that you can change your midi buffers from 250 to 500 and that fixes it ... but it adds a 1/2 second delay to your start time when you hit the space bar to play your project.
I always start my projects quite a few measures in anyway because of track alignment.
Long story short ... audio tracks don't line up very well if you start at 0 measure (referring to Record Latency). I noticed this in Sonar one time when I was trying to manually adjust my Record Latency. It drifted randomly if I started my tracks at 0 measure, so from that point on I started 8 or so measures in. Probably something to do with buffers and all that.
I would never start a project at 0 measure even if I didn't know about the Record Latency drift ... but that's just how I work, probably not the norm.