Adding default GUI theme breaks editor

[bogdanaslt]

Godot version:
3.1.2

OS/device including version:
Windows 10
Fedora Linux 31

Issue description:
When adding default GUI theme in Project Settings and restarting engine autocomplete in editor stops working. On Fedora in theme editor couldn't add new Class Item (dropdown showed only Items I had already added)

Steps to reproduce:

1. Create new GUI theme
2. Go to Project -> Project Settings, under Gui/Theme set newly created theme as "Custom"
3. Restart engine
4. Switch to "Script" tab and start typing some function (func _process()) dropdown is not visible, but clicking up and down and then pressing Enter it is posible to choose some function
5. Go to theme editor, click Edit theme -> Add Class Item. Type dropdown shows only items that were added when creating theme

Minimal reproduction project:
Don't have at the moment

[KoBeWi]

Duplicate of #20123, already fixed in 3.2

[badunius]

Not fixed
Just reproduced it 3.4.4-stable-win64

[Calinou]

Related to #33902, #48477 and #58379.

@badunius Please open a new issue with a minimal reproduction project attached after checking the above issues.