Just wanted to officially report this as a bug here on the bug tracker. Some more details in the links below:

http://forum.mctcp.com/t/terraincontrol-for-spigot-1-10/1011/44

https://www.reddit.com/r/biomebundle/comments/4qh9jz/bug_report_dont_know_if_its_an_terraincontrol_or/

I can confirm that there is no error in the log concerning level.dat corruption (as first suggested by rutger).

The bug is easily reproduced by loading up Biome Bundle in Spigot 1.9/.1.10 as it happens every time the server is restarted. (if doing so be sure to change population bounds check to false to stop the tripwire bug crashing things).

After more testing of workarounds for this issue it has been discovered that specifying a seed in server.properties seems to prevent it. Hope that helps in narrowing down the cause :)

Edit: Actually, it does not seem to prevent it entirely I still have some users reporting it.

yes, actually this issue is not solved even with defined seed in server.properties

After some tests, I can say the bug appears between build 115 (1c7e84d) and 120 (6a03ea2).
Before 115, I always get the same /tc map result and after 120, I always get different /tc map result at each restart.
I cannot be more precise because of crashes in these intermediary builds.

Thank you very much, that narrows down the search considerably. All changes between 120 and 115 are:

1. Fix ReplaceToBiomeName not working bce4c34
2. Don't automatically sort resources queue 91fe6bc
3. New biome: The Void ca094ff
4. Fix another bug in ReplaceToBiomeName ae33ee8
5. And fix another bug in ReplaceToBiomeName d945f36
6. Forgot one line of code 6a03ea2

If I just look at this, I would guess it has something to do with ReplaceToBiomeName... That's not at all where I expected the bug to be.

I checked out bce4c34 and apply patches of commits d945f36 and 6a03ea2 (to prevent the crash I got) on it and the bug occurs so it would be in one of these 3 commits.

And I can confirm that revert these commits on last snapshot fixes the bug.

I tried last SNAPSHOT (I compiled from this repo) version and I got the same issue (despite 9f5dfac).

See generated TC map results for seed 6521433701164005167 :

As you can see, biome borders are nearly the same but not biome types.

are there any news on solving this? thank you :)