Ok, I figured it out.
Marlin outputs the temps while M109 is heating up. Since I am using Octoprint to run my print jobs, it is timing out during the cool down because there is no output from the firmware until the temp is within a few degrees of the target, then M105 replies start coming back. Octoprint is assuming a timeout and dumping the connection, that leaves the last command received by the firmware the M109 and why none of the remaining gcode is run because Octoprint bailed.
I tried putting M109 and M140 into long running commands, but the default time for is still too short. I can bump the timeouts way up to avoid the issue, and will for a short term fix.
Is there any reason why the temp is not sent via the serial connection during M109?
I found the following discussion, but I don't see that anything came of it. I could send a PR for the change if desired. It would be very useful to see the temp during heat up via the serial connection.
http://forums.reprap.org/read.php?146,612559