Same problem after re-installation. I've selected Scala IDE 4.4.1 in the dialog.
2016-05-25 15:13:41,748 ERROR [main] - System.err - [org.eclipse.jdt.launching] error can't determine modifiers of missing type org.eclipse.pde.internal.ui.wizards.imports.PluginImportHelper
when weaving type org.eclipse.jdt.launching.JavaRuntime
when weaving classes
when weaving
[Xlint:cantFindType]
2016-05-25 15:13:41,837 ERROR [main] - System.err - [org.eclipse.debug.core] error can't determine modifiers of missing type org.eclipse.pde.internal.ui.wizards.imports.PluginImportHelper
when weaving type org.eclipse.debug.core.ILaunchesListener
when weaving classes
when weaving
[Xlint:cantFindType]
2016-05-25 15:14:21,941 ERROR [main] - System.err - [org.eclipse.jdt.debug] error can't determine modifiers of missing type org.eclipse.pde.internal.ui.wizards.imports.PluginImportHelper
when weaving type org.eclipse.jdt.debug.core.IJavaLineBreakpoint