Windows 10, GTX 1660
version: 2.83 (sub 7), branch: master (modified), commit date: 2020-03-10 07:58, hash: 1aa7c4c28a06, type:
build date: 2020-03-10, 08:52:15
Within the Preferences Editor, you can change the ordering of various sections but the changes are not retained when you close the Preferences Editor.
The ability to re-arrange sections within the Preferences Editor doesn't seem to have existed in Blender 2.79b but the functionality for re-arranging Panels in the Preferences Editor and the Properties Editor looks to have been introduced into Blender 2.80.
I've just checked with version 2.80, and the changes that you make within the Preferences are similarly not retained when you close the Editor or click 'Save Preferences' prior to closing the Editor.
As for retaining the Preferences order, I'm sure it was the consideration that such changes were retained.
I'm sure this was the consideration for the same functionality available within the Properties Panel, although I'm not sure to what extent changes there are retained.
I don't think this is even technically supported, I would have to look, what is saved un userpref file, but I think it's only field values, and regions are created on the fly.
I don't think this is a bug.
The position of the panels is saved in the region.
Whenever you close a window these regions are released.
When you open a new window, new copies of the regions are created and the default position of the panels is reloaded.
You can have more than one Preference window at the same time.
If you change the position of the panels of one, but don't change that of the other window, what position should be saved?
I think this works as designed.
@Julian Eisel (Severin), you must know this area better, what do you think?
@Germano Cavalcante (mano-wii)'s analysis seems correct. We don't keep around screen (bScreen) data from closed temporary windows, although it would not be that hard to do. There are indeed questions of how to handle multiple Preferences windows.
Anyway, will tag this as known issue with low priority. It's an annoyance but doesn't prevent you from working.