I just tested the "Save as Startup Design" option using AudioLabel 6.0 (Build 6) on Windows 7.
After creating a disc label with images, I clicked the "Save as Startup Design" option and then closed AudioLabel. When starting AudioLabel again, the default label is selected in the "New Project" window.
If the "Show this window at startup" is option is turned off on the "New Project" window, then AudioLabel with load the last saved startup design.
It should be noted, that the "Save as Startup Design" option does not save the text for the Artist, Title, and Track List (unless the "Text Linking Off" property is set for the text). However, if you add a genric "Text" box to the label, the text will always be saved.
Are using a different version of AudioLabel, or a different version of Windows?