Chunk corruption

Hello, my server has been getting more and more corrupted chunks everytime we run a region fixer tool, first it was just 5 then 16 and now 36. I’m wondering if there’s anything I can disable in sponge that edits the terrain in anyway or pixelmon. We have the world pre generated as well. Thanks in advance

Spongeforge: 1.8.9 1693
Forge: 1.8.9 1902

We’re experiencing the same issue on SpongeForge 1692 (recurred on 1689 and 1688 previously as well)
1.10.2

Forge 1.10.2 2073

Some specifics on what tool you’ve been using to fix chunks would be helpful.
It’s possible that recent changes in Sponge worldGeneration stuff might be messing things up.

Thanks I forgot to link the tool here it is http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-tools/1261480-minecraft-region-fixer