Serial Error Pololu Micro Maestro
The MC33926 IC is the PWM motor control driver. Since it's rated for 5A, you can expect it to get hot. (That's 25 watts at 5V, inside a small IC package, which means high temperature.) It can operate to 150°C provided that there's adequate heatsinking, and has built-in thermal shutdown at around 175° and above.

The reason I left a comment about a schematic is because the diagram you posted is not clear about what pins are being used on the motor drivers and microcontroller, etc. As-is, it requires anyone reviewing it to go look up the pinouts of the various parts. It's better to show the distinct, relevant connections and leave out all of unused bits. For example, how am I supposed to know exactly how you connected the JRK controllers to the motors?

Here's the Pololu diagram for the JRK 21v3 USB Motor Controller. (Is this even the one you're using? They make a lot of them.)



Your diagram makes it look as though the motors are on different pins of the header rather than the screw terminals labeled "A/B motor outputs."



Here's my expectation: The MC33926 is getting hot and entering thermal shutdown. At that point, serial communication fails because it's, well, shut down. (Since you say you can run the project for a few minutes, I'm assuming that the communications wiring is correct.)

What is the motor doing? What kind of motor is it? Is it loaded? Stalled? Is the controller rated for the motor current? Have you measured current draw on the motor(s)?

Possible fixes:


Check current ratings on all components, make sure you're not pulling more than the controller is rated for.
Check that the motor isn't stalled or over-loaded. If it pulls the max-rated current, it will drive the controller temperature up.
Consider adding heatsinking or active cooling (fan) to the controller if the above things are in spec.
You might need a more robust controller.


Hopefully this helps somewhat, but more information is needed to be more specific. (You should edit your question to include more info, such as a schematic.)