As my original post says it's a bug in cowtool. The WK leg is deemed by cowtool as ineligible for SQx, hence the SQD calculation doesn't include dollars allocated to that leg. (Admittedly I almost had a heart attack when I loaded my PNR in cowtool and thought I fxxked up, but after conducting a further investigation I found Adam Smith has confirmed LX flight operated by WK counts in this post.)