What is the problem?
The problem is that package upgrades, or, more correctly, software upgrades, do not take into account, sometimes, the existence and handling of existing user configurations from previous versions. These usually reside in ~/.config or dconf.
This problem was raised some detail as a topic suggestion for Ubuntu Desktop 12.10.
What can be done?
We need to learn, to investigate this phenomenon. So two things can be done:
Tag these bugs to collect them like Pokemon
Identify the causes
Collect configuration files with Apport and run automated tests on the applications with those.
This could primarily help to identify some crashes. The collection itself is a good practice and will improve the Apport facility.
1. Tagged Bugs
Bugs are tagged configuration-upgrade. Please help tag those bugs if you know or come across them.
2. Identified Causes
These is where different common causes of our type of bug are categorized and explained. Please add your observations!
Desired Defaults Ignored due to Existing Configuration
This phenomenon occurs when the new version has some new defaults, which are usually desired, and these defaults are overridden by the existing configuration.
This can lead to "missings" features, which would otherwise, in a new user account, be present.
When a new version doesn't take into account some of the old version's configuration matrix then this could lead to crashes.
Different types of crashes can be identified if you like.