I am sorry to hear your rejection! I have the same problem as I found in my CAIPS notes that they didn't award me any adaptability points, neither for my Canadian son nor to my spouse education! But I thought they may update the adaptability points in Ottawa later, after I read your story I became really concerned. So do you mind sharing their email with us? Regarding to the updated reference letter, I think you can easily figure out whether they counted it or not from your total experience points.
Send them an email ASAP; don't wait for their response, go to your MP with your supporting documents that shows your right in those 5 points. I think your appeal will be approved and Ottawa's decision will be reverted, as you applied before May 2013 so those 5 points should be granted easily!
Good Luck
Edit: Quot what is written in OP 6b
9.15. Adaptability
Pursuant to R83, the officer will assess the application and award a maximum of 10
adaptability points, as follows:
a) Educational credentials of the accompanying spouse or common-law partner: 3,4 or 5
b) Previous study in Canada: 5
c) Previous work in Canada: 5
d) Relatives in Canada: 5
Award five points if the applicant or accompanying spouse or common- law
partner has a relative (parent, grandparent, child, grandchild, child of a
parent, child of a grandparent, or grandchild of a parent) who is residing in
Canada and is a Canadian citizen or permanent resident