To reproduce:
1) Create a blank document
2) Drop a VBox
3) Set non null values in the Padding properties
4) Drop another VBox
5) Set non null values in the Padding properties of the other VBox
6) Copy the second VBox
7) Paste
8) Save
    -> the file contains duplicated fx:id in <insets> elements (see attached FXML)

Note that *two* VBox with padding must be created before performing Copy.
If only one VBox is created before Copy, no duplication occur.