Was having similar issues which you described... it seems to happen only when certain Audio Plugins are used on the Instrument Track; in my case its with IK Amplitube. however, i was able to resolve this issue. hope the following helps you too...
1. enable the "Play Audio Tails"
2. when ever you stop the playback, notice the fall in the VU Meters.
3. wait until the Peak has completely disappeared from the meters.
4. when you press PLAY again, you should have everything play as it normally should.
Couple of checks you may want to try...
1. leave the first (1 bar) blank
2. always start on the second (2 bar)
3. play the track until half way and stop
4. rewind to the beginning
5. if you play immediately; you will still hear the tails or a pop
6. if you wait like the above; you should start without any sound (like it all should). notice that on the MASTER and MONITOR tracks, during the first bar, the db number is blank. (ie minus infinity; totally no signal) (once the signal comes in the db number will start jumping)