Just to mention:
After upgrading to 5.6, my editor toolbar - which i customized by adding some extra buttons and different positioning - was reset to the default state.
In addition, all my debug windows which i positioned on the bottom of the GUI disappeared.

This happened before when upgrading from 5.2 to 5.5.

It is known behaviour.
GUI layout can not be preserved during upgrade from one version to another.
See this FAQ post: http://forum.nusphere.com/mini-faq-install-and-settings-t3328.html and in particular this phrase "Layout will be dropped to the default".

Although layout is always preserved when update is made from one build to another (for example from 5614 to 5617) while the version is the same.

Yes that is, but the first time you close and reopen the editor, your settings are lost again.
The second time they get saved. I experienced the same problem 2 times on 2 different PCs
Not a big deal, but I just wanted to mention it.