Yes it's very straightforward actually.
When the chronograph is running, it adds load to the watch so it requires more torque to stay running than it does when the chronograph is switched off. As the mainspring in the watch winds down, the level of torque drops off, and when the torque is not sufficient to keep the watch running it stops.
Since the torque required is higher when the chronograph is running, the spring reaches a point where it can't power the watch anymore earlier than it would when the chronograph is not running. So say it stopped with 6 hours power remaining on the mainspring, and when you stopped and reset the chronograph, that additional load was removed, and now the torque from the mainspring is enough to run the watch again, so it starts running.
It will continue to run until it reaches the point again where the torque being delivered from the mainspring isn't sufficient to keep the watch running, and it will stop. Note that the mainspring is not fully unwound - in most watches it never gets fully unwound so watchmakers like me always make sure we take the remainder of the power off the mainspring when we disassemble the watch for service,. If you don't let down the spring and remove the wrong parts, damage can be done with the power that is still on the spring. In a good condition watch, there will still be around one turn of the ratchet wheel or so left on the mainspring when it's run down as far as it can.
So what you are seeing is normal behavior.
Cheers, Al
