Minecraft – What server config do I need to get monsters to not spawn in the main world, but to spawn in the nether

Only ops are able to program command blocks, so that should narrow the list of suspects. Some (virtual) face time with your ops should reveal the guilty party.

In the meantime, if your map doesn't rely heavily on command blocks, they can be disabled by setting enable-command-block=false in the server.properties file and restarting the server.

To locate the offending block you can render the world map showing just command blocks and redstone, using one of the many 3rd-party cartography tools. (I quite like Minecraft Overviewer for this use, and though it's not technically 1.4.6-up-to-date, it can handle Anvil and custom block IDs so it's still compatible.) This will give you a high-level view of the problem and let you zero in on the possible culprits. Compare it to a regular overworld render to find a recognisable landmark nearby, then fly/tp there, unearth it, and render it inoperable.

When a Craftbukkit/Minecraft server suddenly crashes/loses power, it will attempt to save all currently loaded chunks, if one of these chunks is inproperlly saved then it will Regenerate that chunk based off the world's Seed.

You can prevent this from happening again by updating/removing all outdated plugins, correctly shutting down the server in the future and if this issue is that big of a problem, providing the server with a auxilary power supply giving it enough time to correcly shut down if such event should happen again.