It was me and simply inexperience as I've only been playing minecraft for just over a week. Never any lag when I was on with all my stuff running for a hours and hours, so it could easily have been the water as that's the only thing that 'changed' from my previous quarry setups? I just used 2 water sources instead of 1. The quarry itself was keeping the same number of chunks loaded as the default sized one (2 chunks kept loaded as per the message.) It was my first time trying out markers and doing an 18x9 quarry instead of a 9x9.
Had set the water source at the beginning of each quarry (Have done over a dozen now) based on advice on how to set up automatic quarries from forums and other TOG players so I 'thought' I was doing it correctly and safely.
Lesson learnt and I deeply apologise for impacting on the time for all those involved who had to go in there and break the break (as it were.) Can't have been easy avoiding monsters while at it.
For what it's worth for others, it doesn't appear too heavy handed an approach but I have to inspect everything to find out for sure