Probably this is related to the changes done by Jens to support preserving the splits in the layout.
The issue with the example project of the OP should be fixed in trunk.
It was indeed, because of missing source-files, with fileOpen-attribute-set in the layout file.
After some closing and opening, it ended with several fioles with the same tab-position.
And this seems to lead to a corruption in cbauibook::LoadPerspective().
I also changed the SavePerspective()-code in a way, that a project layout-file only saves the tab-layout of files belonging to the project, and that the tab-layout of files not belonging to any project is no longer saved.
Workspace-layout files should save the tab-layout of all files belonging to any project.