I there some type of thermo cut off or limiting feature on either the software or the E flight motor? Seems today as I was flying and my motor got hotter it was cutting off and then going again? Any reason for this?

Robert,

It may well be the ESC that is over heating as Crist suggests. Also make sure all connectors are good and that there are no loose wire (poor connectors). There have been reports that the banana plugs that are attached to the motors at the factory are some times poorly soldered. If you are running a Phoenix ICE ES, you can check the data to see if that tells you what is happening.

Yes, go hunting for a bad connection first, in a case of odd behavior like this.
Tuner cleaner is a good weapon, too.
How hot are the components when you land?
Yes the logger in the  ESC will tell you its own max temp, but it warns you as Crist said.

Also be wary of having any of the low current wiring (like the timer to ESC wires) running too close to the high current wires at either end of the ESC.
Noise coupled from the high current wires can confuse the ESC input and it sometimes responds by politely sitting on its own hands.

later,
  Dean