Ah,
now I see where the problem is. Yes, each setting is saved on a project and user basis. Originally, the main thinking behind this was that some users create different projects for different reasons. For example, one user created a project exclusively for managing scripts and therefore wanted the script explorer to be prominent. So we went with saving the layout on a project basis.
However, you can specify that you want the current layout to be the default layout for all projects. You can do this by selecting Tools > Make Current Layout Default. This layout will then be applied to all new projects that are created.
We should add an option to apply the current layout to existing projects but there is a quick workaround that you can do if you want to apply the current layout to each project now.
Make the current layout default as described above. Then browse to "...\My Documents\SQLDBControl Projects\". Make sure there is a DefaultLayout.xml file in this folder. Now, each project has its own folder in here and within each project folder there is a Layout.xml file. If you delete the Layout.xml file in each project folder then, on project startup, the default layout will be used.
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