Thanks for the answers, however none of them helped to solve the issue.
I do not have ATI Hydravision installed
I do use dual monitor setup
I am using the machine with administrator rights, so the registry access should not be the problem (after deleting the key it was recreated)
But, when experimenting a bit with the application, I can describe the symptom hopefully better:
This issue occurs only when I close the application maximized.
Next start shows the app window maximized with history and layer windows in the center
Restoring the app puts them properly to the side
Maximizing again - the windows stay on the side