You see, flatland worlds are somewhat strange. When you initially spawn on single player, you spawn at a random coordinate that could be in the thousands. Many people complain about how when they die, their spawn point is completely changed, to be thousands of blocks from their first one. What may be happening with you is Multiverse is spawning you at the standard 0,0 coordinate (push F3 to check). The world is probably not completely flat, rather, you'll have to fly far away to find you building. To do this, first open your world in single player. Press F3 and memorize/write down the X and Z coordinates. Then go back to your server and go to those coordinates. If you have Essentials, you can do /tppos X 64 Z. If you find your building, then reset the spawn of your world.
In summary, I think that your building is in that "completely flat" world, just far away, so you can reset your spawn to it. I'm not guaranteeing that this is correct, but I hope this helps!