Might have broke the server, here's how to fix:
To the north of spawn and a little to the left in a biome corner I have my quarry. It's activated with a Redstone signal, just delete the wireless receiver on the top to stop the Redstone signal and the quarry should immediately stop.
EDIT: reason for this is because the quarry is mining chunks that the server hasn't generated yet, normally the quarry can go slow enough that the server can keep up with the chunk generation but my quarry is running on supercharged power so it goes much much faster than even MPS jetpack flight, I overestimated the server speed. Cut off the redstone signal in MCedit and it should turn off.