It looks like you have a dynamically named index field:
<input id="<?php echo($SiteSettings->getColumnVal("SettingsID")); ?>" name="<?php echo($SiteSettings->getColumnVal("SettingsName")); ?>" type="<?php echo($SiteSettings->getColumnVal("SettingsType")); ?>" value="<?php echo($WAGlobals->getColumnVal("SettingsValue")); ?>" class="form-control control-group" tabindex="<?php echo($SiteSettings->getColumnVal("SettingsWeight")); ?>" title="Please enter a value." required="true">
It shouldn't be... it should just be:
<input id="setting_<?php echo($wa_startindex); ?>" name="setting_<?php echo($wa_startindex); ?>" type="text" value="<?php echo($WAGlobals->getColumnVal("SettingsValue")); ?>" class="form-control control-group" title="Please enter a value." required="true">
Then you don't have a binding set to update that column. You would need to update the code above from:
$UpdateQuery->Table = $MultipleUpdateTable;
$UpdateQuery->addFilter($MultipleUpdateIndexColumn, "=", $MultipleUpdateIndexColumnType, $_POST[$MultipleUpdateIdentifier."_".$MultipleUpdateCount]);
to:
$UpdateQuery->Table = $MultipleUpdateTable;
$UpdateQuery->bindColumn("SettingsValue", "s", "".((isset($_POST["setting"."_".$MultipleUpdateCount]))?$_POST["setting"."_".$MultipleUpdateCount]:"") ."", "WA_BLANK");
$UpdateQuery->addFilter($MultipleUpdateIndexColumn, "=", $MultipleUpdateIndexColumnType, $_POST[$MultipleUpdateIdentifier."_".$MultipleUpdateCount]);