do they open properly if you open them from finder?
Is this a problem with switching to a running application, or with starting an application that is not running?
grant: i'm waiting for it to fail again to check the finder or 'recent apps' route.
john: program is running already, but clicking on dock icon does nothing to bring it up onscreen.
Does Cmd-TAB behave differently?
neither cmd tab, nor finder will bring the apps onscreen (though they are active).
Definitely one of the first things you should do (apart from trashing your Indesign preferences) is to close all but the system fonts and see if that improves things.