For some reason, after installing the patch now it seems to always reset the value in the INI file to whatever I just put -- i.e., I change the value in the fullscreen/windowed mode line to "ask," but it only asks once. After that, the value in the INI file is whatever I'd selected before. (So if I say "no," to fullscreen mode, it changes the value to zero and always runs windowed mode.)
This worked fine before the patch. Anybody else having this issue?
EDIT: Just found other posts that indicate that yes, 1.09 seems to have broken this. Let's hope they fix it in the next patch.