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Another way of fixing the stronghold problem which I didn't think of earlier - Opening the map in MC edit and simply deleting the chunks where the Stronghold is meant to appear. Then they should re-generate properly next time someone goes there.
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That would work, but I still have no clue what's causing the seed to fuck up every time.
Edit: Server seems to have crapped itself again and is stuck starting up, apparently. I've sent in a support ticket, hopefully they will deal with this soon.