This problem had been bothering me for a while and I couldn't work out why the quarries and pumpjacks were producing excessive amounts. Today I spent a couple of hours fiddling with the config, planting quarries, testing, but it didn't seem to make much of a difference.

Eventually I worked out it was another plugin, GatherManager, that was causing the issue. (D'oh!) I set the values for quarries and pumpjacks to 1 in GatherManager for my PvP servers, and everything is working as it should. (I've left PvE at x5 which fine for that server type.)

So if you have this same problem of too much output, go check your GatherManager settings. ;-)