> How did you print the list of all manually installed packages? What > was the command you used?
I use the command aptitude search "?and(?installed , ?not(?automatic))" (probably more awkward than it needs to be -- I haven't bothered to seriously read the manual) I have attached the unabbreviated text of the session. If you can suggest some tests to run on my system, I'll see what I can do. Or I could tar up any relevant directories and send to you, if that would be any help.
aptitude-markauto
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