I always get the following error when trying the default update site.
It seems like a very similar error but not the same, the IPv4/6 flags doesn't help.

!MESSAGE Unable to access "http://download.eclipse.org/eclipse/updates/3.5".
!STACK 1
org.eclipse.core.runtime.CoreException: Error parsing site stream. [The XML stream is not a valid default "site.xml" file. The root tag is not site.]
        at org.eclipse.update.core.Utilities.newCoreException(Utilities.java:225)
        at org.eclipse.update.core.Utilities.newCoreException(Utilities.java:256)
        at org.eclipse.update.core.model.SiteModelFactory.parseSite(SiteModelFactory.java:95)
        at org.eclipse.update.internal.core.SiteURLFactory.createSite(SiteURLFactory.java:80)
        at org.eclipse.update.internal.core.InternalSiteManager.createSite(InternalSiteManager.java:334)
        at org.eclipse.update.internal.core.InternalSiteManager.createSite(InternalSiteManager.java:326)
        at org.eclipse.update.internal.core.InternalSiteManager.createSite(InternalSiteManager.java:298)
        at org.eclipse.update.internal.core.InternalSiteManager.attemptCreateSite(InternalSiteManager.java:222)
        at org.eclipse.update.internal.core.InternalSiteManager.getSite(InternalSiteManager.java:162)
        at org.eclipse.update.core.SiteManager.getSite(SiteManager.java:82)
        at org.eclipse.update.search.UpdateSearchRequest.searchOneSite(UpdateSearchRequest.java:454)
        at org.eclipse.update.search.UpdateSearchRequest.performSearch(UpdateSearchRequest.java:325)
        at org.eclipse.update.ui.UpdateJob.runSearchForNew(UpdateJob.java:183)
        at org.eclipse.update.ui.UpdateJob.run(UpdateJob.java:171)
        at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: org.xml.sax.SAXException: The XML stream is not a valid default "site.xml" file. The root tag is not site.
        at org.eclipse.update.core.model.DefaultSiteParser.handleInitialState(DefaultSiteParser.java:393)
        at org.eclipse.update.core.model.DefaultSiteParser.startElement(DefaultSiteParser.java:198)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:504)
        at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:376)
        at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:602)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3080)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:899)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:625)
        at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:488)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:819)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:748)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:123)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
        at org.eclipse.update.core.model.DefaultSiteParser.parse(DefaultSiteParser.java:154)
        at org.eclipse.update.core.model.SiteModelFactory.parseSite(SiteModelFactory.java:83)
        ... 12 more