When changing some of the options in V1.48B, the "Apply" button remains grayed out and inactive. This behavior occurs at least for the option "Don't Replay after Backwards Frameskip". Most other options seem to work fine, but I am not sure whether this is really the only buggy option.
Work-around for now: Exit the options menu via the "OK" button. The new option settings will be saved this way, too.
Thanks to möbius for noticing this bug.