I deleted the chunk files (server\world\region\r.0.0.mca, etc.), beacuse i would have like to prepare a new region in everywhere (except in my homeland), and later i dropped an Eye of Ender to find a stronghold. I went to location where the eye directed, and dug out the entire area. The eye just hovered in the air, where there was nothing. I revealed all of the area, but I did not find the stronghold.
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Seed: -644880586686743976
Coord x: 747, z: 87
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I have a similar problem.
Started the map in 1.5.
Walked around the whole map at lowest zoom level – all stronghold must have been spawned.
After the update to 1.7 the eyes of ender point in different directions.
I also discovered that the seed now generates a different map than before.
I cannot say since what exact version this happens.
But I took my world from the server and tried it in single player creative mode. Couldnt find a stronghold.
Regenerated the map with the same seed, and found a stronghold immediately.
Please provide seed and coordinates.