If I do a two-finger gesture, it takes about two seconds until the Firefox window scrolls, and then it is immediate and not an incremental scroll.
Is this a known issue? Could it be a plugin (I don't have anything too non-standard)?
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Try creating a new profile (http://kb.mozillazine.org/Profile_Manager#Mac_OS_X), if the issue is not present with the new profile than very probably your current profile is in some way "corrupted", maybe because of some extension.