Created attachment 124479 [details] stack trace that shows the non-starting eclipse issue
The rebuild-sdk-features script does not work when updating from 3.1.1 to 3.1.2. There are references to 3.1.1 features in org.eclipse.sdk/feature.xml that shouldn't be there. Also, there are references to the rcp feature and/or source feature in org.eclipse.sdk/feature.xml but I think this should only be refernced in org.eclipse.platform/feature.xml because the platform includes the rcp not the sdk. These two issues cause Eclipse to not start the second time it is used (see attached stack trace) unless the -clean option is added to the commandline. I manually edited the feature.xml files to remove the references to both the 3.1.1 features and the rcp feature and the problem went away.
This is fixed in rawhide as of 2006-02-11.