Mame32, ah...
Mame32 rewrites the ini every time you change any settings. This is a
mame32 feature; official mame doesn't do this.
I don't use mame32 much, but it's possible 0.88 doesn't have that option in the settings windows in a box to check/upcheck. If not, then mame32 doesn't have that setting to write, so it's "removed" from the ini.
Try to find that settings in mame32's settings windows; if you can't find it, well, there's only a few things to do:
Never open mame32 settings.
Make your ini file read only.
Try a newer mame32 and see if this option was added. (If not, see above two...)
