Microsoft Group Chat preference settings gets downloaded from the server to the User's appdata folder for the Brand new user .
If we have customised the setting and copied the same preference file to user's appdata through the package, it will be overwritten when you launch the application. In order to overcome this Issue we may need to create two active setup keys that checks for the file under User's appdata and delete the other active setup keys if file is not present, this way we are making the active setup to run once again, this is a loop based installation.
Activesetup 1 will run, check for the file, if present don't do anything, if not delete activesetup2 hkcu key so that it triggers active setup 2
Activesetup 2 runs check for the file, if present don't do anything, if not delete activesetup1 hkcu key so that it triggers active setup 1
If we follow the above logic we might be able to resolve the issue.