That was my first thought, but no. There are no punch, loop, or other controls enabled. Unless there are deeper functions within the configuration file (?). It appears to be completely random. And the record in/out does not happen in the same place every time.
Here's a little more info though. My OP was typed on my way out the door (my apologies for being a little light with the details).
It started acting this way after I installed X3E. At first, I thought I was doing something by accident - like hitting my mouse or keyboard. In addition to the gaps that appear while recording, the regular normal play back appears to start itself. When taking a potty break, my computer started playing on its own. And it would do things like things repeatedly.
After ruling out punch-in features, I thought maybe my keyboard or mouse or KVM switch might be acting up. I removed all three and tried a brand new keyboard / mouse with new drivers. Same thing.
I only started to suspect Sonar this afternoon, so I don't have enough useful info to submit a bug report yet. I was just hoping someone else might've seen this too.