Insulation Voltage of Aluminum PCB - With and Without Electronic Components
The difference is most likely in the method of test. Looking at the wires in the two pictures with most everything being the same, its probably the crap between the wires. 

I'll bet that if you took only the top board and connected the wires, then did the insulation test, and repeated the test several times, the answers would vary even with no LED's connected. 

Either keep the wires consistent between tests, or make sure they are connected in the same way as possible. Clean off the residue between the contacts with flux remover.