Trying to figure out why my systems render times are so different
System 2 is using GPU acceleration, System 1 is using CPU rendering.  GPUs, especially Quadros run many rendering tasks FAR more efficiently than a general purpose CPU.  It could easily explain the difference of 83% CPU utilization and 40 minutes of render time.

Note that while your system is showing only 14% CPU utilization in the screen shots, that is 100% of a single threaded process.  If the calculation isn't broken in to multiple threads, then it has to process on one core of the processor, which appears to be what is happening here.  That one core is completely maxed out.

I see you have CUDA selected as the renderer in the second screen shot, however it is not being used based on the GPU usage information.  This is probably related to a driver issue preventing Media Encoder from being able to utilize the GPU hardware.  Try updating your graphics drivers and verify that your graphics card appears on the list of supported graphics cards for CUDA support.