This use case is taken from the old GRECLIPSE-1755, but the symptom is different.

Create a Groovy project which depends on org.hibernate:hibernate-core:3.5.6-Final and write the following class:

package f

import org.hibernate.SQLQuery
import org.hibernate.SessionFactory
import org.hibernate.impl.SessionFactoryImpl

class F { 
	static main(args) { 
		SessionFactory sf = new SessionFactoryImpl(null, null, null, null, null) 
		SQLQuery query = sf.currentSession.createSQLQuery('SELECT BLA BLA') 
	} 
}

When I opened GRECLIPSE-1755, Greclipse was confusing org.hibernate.Session.createSQLQuery(String) with org.hibernate.classic.Session.createSQLQuery(String, String, Class), which is deprecated, and hence it was showing my method call with the deprecation highlighting.
This does not happen any more, but what I see now is that I can't navigate to org.hibernate.impl.SessionFactoryImpl.getCurrentSession() (by hitting F3 on currentSession) or to org.hibernate.Session.createSQLQuery(String) (by hitting F3 on createSQLQuery). Eclipse does nothing, apart from writing "Current text selection cannot be opened in an editor" in the status bar.

By the way, I noticed a lot of such problems in one of our main projects, but it's hard to extract a small and sharable use case from there. While trying to reproduce GRECLIPSE-1755 I could finally reproduce this behaviour, I hope you'll be able to reproduce as well.