Recently I found a problem with running a BuildCraft Quarry on a server.
The Quarry tends to not want to mine Iron, Redstone, and Emerald. Seems to be fixable after a server restart. But constantly restarting the server to fix this isn't a definite fix. Nothing I'm aware of is randomly causing the Quarry to stop mining the ores. Mines all the modded ores with ease.

Do you know if you have other mods installed? I have the same issue and determined that a mod Reskillable is causing it.