Error when Upgrading MOSS 2007 from SP1 to SP2

When I try to upgrade it fails at around step 8/9 and here is my error:



[SPManager] [DEBUG] [8/18/2010 9:31:58 AM]: Elapsed time upgrading [Microsoft.SharePoint.Administration.SPIisWebSite]: 00:00:01.
[SPManager] [8/18/2010 9:31:58 AM]: ReflexiveUpgrade [Microsoft.SharePoint.Administration.SPIisWebSite] failed.
[SPManager] [8/18/2010 9:31:58 AM]: There are multiple root elements. Line 15, position 6.
[SPManager] [8/18/2010 9:31:58 AM]:    at System.Xml.XmlTextReaderImpl.Throw(Exception e)
   at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
   at System.Xml.XmlLoader.LoadNode(Boolean skipOverWhitespace)
   at System.Xml.XmlLoader.LoadDocSequence(XmlDocument parentDoc)
   at System.Xml.XmlDocument.Load(XmlReader reader)
   at System.Xml.XmlDocument.Load(String filename)
   at Microsoft.SharePoint.Upgrade.SPWebConfigIisSiteAction.get_AppWPResourcesWebConfig()
   at Microsoft.SharePoint.Upgrade.EnsureWebConfigSettings.Upgrade()
   at Microsoft.SharePoint.Upgrade.SPActionSequence.Upgrade()
[SPManager] [8/18/2010 9:31:58 AM]: Action 3.0.5.0 of Microsoft.SharePoint.Upgrade.SPIisWebSiteWssSequence failed.
[SPManager] [8/18/2010 9:31:58 AM]:    at Microsoft.SharePoint.Upgrade.SPActionSequence.Upgrade()
   at Microsoft.SharePoint.Upgrade.SPManager.Upgrade(Object o, Boolean bRecurse)
   at Microsoft.SharePoint.Upgrade.SPManager.ReflexiveUpgrade(Object o, Boolean bRecurse)
[SPManager] [DEBUG] [8/18/2010 9:31:58 AM]: Disposing Microsoft.SharePoint.Administration.SPIisWebSite.
[SPManager] [INFO] [8/18/2010 9:31:58 AM]: Resetting the status of PersistedUpgradableObject: SPWebApplication Name=SharePoint - 62522 Parent=SPWebService to Online.
[SPManager] [8/18/2010 9:31:58 AM]: ReflexiveUpgrade [SPWebApplication Name=SharePoint - 62522 Parent=SPWebService] failed.
[SPManager] [8/18/2010 9:31:58 AM]: There are multiple root elements. Line 15, position 6.
[SPManager] [8/18/2010 9:31:58 AM]:    at System.Xml.XmlTextReaderImpl.Throw(Exception e)
   at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
   at System.Xml.XmlLoader.LoadNode(Boolean skipOverWhitespace)
   at System.Xml.XmlLoader.LoadDocSequence(XmlDocument parentDoc)
   at System.Xml.XmlDocument.Load(XmlReader reader)
   at System.Xml.XmlDocument.Load(String filename)
   at Microsoft.SharePoint.Upgrade.SPWebConfigIisSiteAction.get_AppWPResourcesWebConfig()
   at Microsoft.SharePoint.Upgrade.EnsureWebConfigSettings.Upgrade()
   at Microsoft.SharePoint.Upgrade.SPActionSequence.Upgrade()
JRose628Asked:
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Justin SmithSr. System EngineerCommented:
you installed wss sp2 first, right?  are you logged in as the farm account?
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JRose628Author Commented:
Had to open an MS case on this.  

Somehow sharepoint kept trying to do an update without user interaction.  Also some missing data in our web.config for mysites.  We ended up deleting mysite database and content(I didnt want mysites anyway).

We also deleted the update cache and set the xml file to 1.  After this ran all updates and provisioned some software and it upated perfectly.  
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