So I'm using FTL from Steam.
Gognak's mod manager v1.5
Installed mods: Beginning Scrap advantage (came with the mod manager and needed to get the resource folders)
Modified save file to get access to all ships
Modifying the Shivan in the ship editor:
Cursor problemOccurs when I load an existing ship from game folder but not when I create a ship from scratch. Is not unique to ShivanHere it is normal: Black arrow shows where my cursor is on the screen

Here is where the my cursor no longer corresponds to where it is in the program. The red arrow is where my cursor is.

Now if I use the direction keys in the program and shift the entire thing down and to the right the mis match cursor area increases.The Red arrow is where my cursor is and the red square now corresponds to the entire area my cursor will be messed up in.
Now for the problem when adding the ship into the gameChanging the Shivan again.
Steps:
-load existing ship from game
-delete all rooms
-make new layout superimposed on base (make sure it matches)
-options -> export ship
-export ftl package
-use mod manager to import ship so I can check in the hangar
Changing doors only:

Result:

Restoring backup
Changing rooms:

Result:
