Snes9x.com

As per subject. The fullscreen option at startup is currently broken. Checking the "Fullscreen" option does not "stick" between loads, and also if I change the "fullscreen" option in the conf file, it simply gets reset at each launch. Likewise, the -fullscreen command-line option does nothing. I'm switching to another emulator as I cannot use snex9x in a tiny window on a cabinet Thought I'd just leave the bug report though! Thanks!

works for me on 1.60 (x64) on win10 - if I'm fullscreen when I close snes9x, it'll be fullscreen next time I run it.

any particular reason you're using an older version?

I am on version 1.62.3 and I am having the same issue for fullscreen not saving after exiting. Including setting it to superscope and it forgets that as well.
All my other options that I have noticed so far is saving properly, like windowed size and video filters and so on.