I have this problem too, but if I go back right into the mod settings and change it again right away, it save on second time around.

I am waiting for 1.1.3 to be released to see if they solve the problem.
I looked up the bug and found a possible fix by jeff. Try this...
In Modsetting.php look for this:
$request = mysql_query("UPDATE {$db_prefix}settings SET value=$onoff WHERE variable='$var' $doLimitOne");
and remove the doLimitOne so it looks like this:
$request = mysql_query("UPDATE {$db_prefix}settings SET value=$onoff WHERE variable='$var'");
Hope that helps?