there are two Skyrimprefs.ini files. on is in C:\Users\?you?\Documents\My Games\skyrim
the other is in C:\Program Files (x86)\Steam\steamapps\common\Skyrim\Skyrim
I checked both of these since I thought there was only one, and found that one of them had the sneaky line "FullScreen=0", which was the cause of the distress. Some of you who are having issues might want to check this, because I had it set to FullScreen in the options, apparently to no avail.