I am currently using ValkiyrienSkies (forge-2.0.0-alpha6) and Eureka (1.0.0-alpha7) and sometimes when I deconstruct a ship, half of it goes down or up by one block(see picture below). After some testing I fugured out that it mostly happens when the ship faces y-axis.

The fix for this issue has already been pushed and will be part of the next Curseforge release.