I think this is the problem if all the instances are sharing the same preferences file.
This is because the last 'instance' to close will overwrite any preferences saved by the other instances.
Multi-instance is really meant to be used where you want each instance to have a separate ini file with possibly different settings.
If you can describe your setup and the way you think you want to work then I can make suggestions for how best to achieve that.
Let me know...