Thanks for responding. I know it is not related, but I found the article HT3662 while searching for that sticky-quarantine problem.
You did solve my first (implicit) question. However, in the AppStore preferences, that option is now probably subsumed under "Install system data files and security updated".
I did find the solution to my second problem (quartined applications not being cleared after first approved opening); it is also in HT3662.
It turns out that I installed some applications from my Administrator account, without ever opening them there. My regular account is not priviliged. Apparently, that makes it impossible to clear the quarantining.
One solution is to log into the Administrator account, open the application there, approve it. Now, the quarantining attribute is cleared, and problem goes away, also in other (non-priviliged) accounts.
Message was edited by: ws_tom_v; added that option was renamed in AppStore preferences.