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It seems to be random.
Created attachment 12718 [details] The exception
It's propably directly in SCO not module system.
The bug is in o.n.m.utilities.Installer which calls searchInstaller = new org.netbeans.modules.search.Installer(); which is illegal since search.Installer is a SCO and you must use SCO.findObject to get an instance. Or you could make search.Installer not extend ModuleInstall; there is no reason for it to.
BTW it would have been nice if upon seeing the line in ide.log Run with -J-Dorg.openide.util.SharedClassObject=0 for more details. someone had actually done so.
Should take five minutes to fix.
Fixed in the trunk. Modified file: utilities/src/org/netbeans/modules/utilities/Installer.java (1.28)