Operating system: Windows-10-10.0.17763 64 Bits
Graphics card: GeForce GTX 1080/PCIe/SSE2 NVIDIA Corporation 4.5.0 NVIDIA 418.81
Broken: version: 2.80 (sub 74), branch: master, commit date: 2019-07-11 13:50, hash: rB06312c6d2db8
Short description of error
User preferences and add-on preferences are normally auto-saved when Blender exits, and it is triggered when the user modifies preferences data through the UI. But there appears to be a bug that prevents this from happening when the preference data is defined inside of a property group.
Exact steps for others to reproduce the error
Write a simple script that adds/draws two preference variables for an add-on: One directly inside of a class derived from bpy.types.AddonPreferences (root preference), and one inside of a class derived from bpy.types.PropertyGroup (group preference). Make sure to include the property group instance as a bpy.props.PointerProperty. During execution, if the user modifies the root preference through the UI, auto-save will be triggered correctly, and both values will be saved on exit. However, if the user modifies the group preference only, neither value will be saved on exit.
A similar issue occurs when preference values are programmatically altered (auto-save is not triggered), but I'm not sure if this is a bug, or lack of a feature.