Vertical and horizontal separation between cruising and climbing aircraft
I think you may have answered your own question note the use of the word OR 


  To my understanding, aircraft at these altitudes should always have a
  separation of least 1000 ft or 5 nm.


If you take a look at your data the aircraft are always separated by 1000 feet OR 5nm. The singular exception to this is when you have the separation quoted at 4.81 miles and 982ft. This can to an extent be explained away by the inaccuracies in systems like FlightRadar24