I would think this is the most popular question and the one with the most number of different answers. According to research I’ve done online and speaking with people this is my conclusion.
You have to submit only the highest degree achieved that you are trying to get points for which in you’re case is PHD this is what CIC themselves states. Also your WES statement states the prerequisite for example for an MS its a BS and for a PHD its possibly an MS or a BS.
http://www.cic.gc.ca/english/helpcentre/answer.asp?qnum=991&top=29
If you read their answer they only say that if you have to degrees like a BS in Comp. Sci and a BS in Chemical Engineering then you need to certify both for additional points and likewise for double PHD’s or MS.
Finally sorry for the delayed reply I was traveling on a holiday and offline for a bit of a tech detox.