I can only confirm the issue and make Robbbert aware of it.
I put MAMEUI64 in an empty folder, then from command-line I executed:
MAMEUI64 -cc as per Robbbert directives.
Then I launched the program, and entered in Default Options. Enabled "Run In a Window" which is by default disabled. Confirmed.
Launched a random game, yes, it is displayed in windowed mode. So the change was taken in account.
Exited, closed the program.
Re-launched MAMEUI, went into Default Options again and.... ta-dah... "Run In a Window" is disabled again. The modified settings was not saved. Or better, it's probably that it was saved the first time I modified it and then overwritten with default values again when I exited the program.
Yes, there's a bug, it seems.
Edited by Mamesick (11/05/15 12:15 PM)