What is happening is that when you add a note that already exists (on another string) Fretspace interprets the shape as an arpeggio rather than a scale (because of the duplicated note).
You can prevent this happening by entering the name manually. If you're starting out with an existing C Lydian Dominant shape:
1. Select the box name and copy it (Command-C)
2. Add a note (Fretspace will change the name at this point)
3. Select the box name and paste back the name you copied
After you have done this, Fretspace will no longer change the name. If you want to revert back to having the name be automatically chosen (when you have finished adding/removing notes) you can select the name a second time and delete it.
You might also find that selecting C Lydian Dominant in the scale finder and choosing "Diagonal" in the "Shape" popup gets you close to what you are looking for.