I figured out what it was... me being dumb...
In my mame emulator setup in LB for autohotkey running script, I had...
$Esc::
{
Process, Close, {{{StartupEXE}}}
}
I switched it to ...
$Esc::
{
WinClose, ahk_class MAME
}
and now the settings save when exiting mame via launchbox/bigbox.... the Process, Close method must not exit mame gracefully and therefor doesn't save anything. hope this saves someone else some time.
thanks everyone for the tips!