New iTunes update, iPod no longer shows up in iTunes

Got a update request from iTunes today and accepted the upgrade for iTunes and QuickTime.  I ignored the warning from Microsoft that this was not approved for XP (stupid, but I doubted that Apple would trash my connection).  After the install, I no longer have my iPod show up in my iTunes.  I have done a System Restore, deleted iTunes and reinstalled, deleted iTunes and manually removed all left over folders and then reinstalled; followed all of the troubleshooting items at http://www.apple.com/support/ipodtouch/assistant/itunes/ and lots of other things over the past 6 hours.  I am really tired now.  Does anyone have any help.  Note that the iPod charges through the ISB port, the wi-fi worksm the apps and music and library items show up in iTunes.  The only thing that is missing is the iPod showing up in iTunes so that I cannot sync.  Also when I open iTunes I get this message:
  Warning!
  iTunes was not properly installed. If you wish to import or burn CDs,
  you need to reinstall iTunes.
I need to sync. Help.

Good news now.  After two more uninstall/reinstalls I now get my iPod showing up in iTunes.  I still get the:
Warning!
  iTunes was not properly installed. If you wish to import or burn CDs,
  you need to reinstall iTunes.
box every time I open iTunes, but this is an annoyance, not a disaster.  Still any help in stopping this pop-up would be appreciated.  Also I have sucessfully imported a CD to iTunes, so I am not sure what the warning is about.  (I do not have a downloaded song to try to burn to a CD however).

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