Hey there, I use the ship editor... a lot.
Since 1.9 and the 2.0 Opt in, scaling behaviors have changed.
1) Make a custom starbase, the starbase model is using an absolute scale and goes off the hex significantly.
2) Attach a part or custom part to a custom part, and scale down the original custom part, it won't always scale the subsequently attached parts as before.
Doesn't seem to affect parts made before the updates though, so it might be something in how the custom part files are saved?
Sorry, its really a wonky one to recreate.