It seems that if the global .ini file exists it is loaded on start, but if it is readonly changed settings are stored in a per-user .ini file. But since the global one exists it is read on start, the old settings are used. So if the global one is deleted everything should work okey.
I wonder why they don’t try to read the per-user .ini file first though.
A new version the application I use to store my passwords and generate new ones has been released.