Is you voxel model totally filled before exporting to elements? Only 1 empty voxelspace inside can make strange things to happen ingame.
Anyway these are the steps i do for an export into Minecraft:
- Make sure the model is filled properly with Voxel menu->Transform->Fill volume (if its doing strange things, check for "holes" in your model)
- Convert voxels to elements using Atlas method
- On the Element toolbar click remove hidden faces and apply new culling (The 2 icons with the lightning)
- Right click voxel_atlas texture and rename it as needed, than save it to the textures folder accordingly.
- Export your model into the model folder
Try these steps if you haven't already, and let us know if it was any help!