After arranging my tabs as follow:
(though in this case even with one column on the very right side more), closing and reopening the project, all 5 tabswere arranged horizontally (one below the other).
If you join more than two tabs under one common tab, you need to decide which orientation (either vertical or horizontal) of the split to choose. CafeTran does not support mixing the orientation when joining more than two tabs. Of course, you can mix it for the current session but their state is saved in preferences with one orientation. Try joining your four tabs separately into two groups (one with vertical and the second with the horizontal split). Then CT will remember their state. You can dock the joined groups to have them in one view.