I think the GUI customizations are saved in the configuration folder. Unfortunately new installation has to set up a new configuation (reusing old configuation may have compatibility issues). Maybe you can try to export/import your preference and see whether it works for you.
That should work for you. Use File/Export/General/Preferences. I've done a quick test and taken a look at the file that is produced (plain text). It lists the iTest preferences (and general Eclipse preferences as well) that I've customized.
I've tried exporting that file, editing it, and re-importing it. It doesn't work in either 3.4 or 4.0. Maybe I'm just editing it wrong; I'll have to look up the format.
Is it possible that one has to restart iTest after importing preferences for Window layouts, etc... or even do "Reset perspective..." because perspective is already initialized with old values and preferences are being imported later.
