The updater should be working now, I just checked.
Confirmed, still doing the same thing.
Add to that you can stop the scan after its started or Spybot just freeezes up and you have to kill it with task manager. Its all about the new release.
Can you try a full uninstall and reinstall it and see if it works? Download a fresh copy:
http://www.safer-networking.org/en/mirrors/index.html
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Uninstall Spybot, reboot, delete the Program Folder and proceed with installation.
I was having the same problem on my Vista machine as the OP but not in my XP machines. I was getting the Warning window that said "Please select some update files from the list first.", but there was nothing to select.
I tried downloading a fresh copy, uninstalling Spybot, rebooting deleting the Program folder and reinstalling. This still didn't solve the problem.
This morning I had the Ah Ha to try setting the compatibility mode on SpybotSD.exe to XP service pack 2 (the only option I had).
Voila no more warning window.
Hope this help.
Getting an answer is one thing, learning is another.
Microsoft Windows XP Home Edition running on a 2.40GHz IntelŪ PentiumŪ 4 Processor with 512 MB of RAM and a 533 MHz System Bus.