Yes, I experienced the same thing after removing evolution (an insanely slow app).
"apt-get install $pkg" does not clear this flag
"sudo apt-mark unmarkauto $pkg" does the trick.
usage: apt-mark [options] {markauto|unmarkauto} packages...
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apt-get install $foo should clear the autoflag for $foo
https://launchpad.net/bugs/72007
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