MapleDream, I and all of us really do appreciate you sharing this information. It is too bad that they don't really consider you having completed a program of two years study, despite the fact that you have completed more than two years of PhD in Canada. You can probably try contacting, telling them that you have completed more than two years of study at a post-secondary institution in Canada by trying to do the following:
http://www.canadavisa.com/canada-immigration-discussion-board/how-to-deal-with-an-unfair-ner-a-negative-eligibility-review-t67741.0.html
Tell them that, according to OP-6, and also the instruction guide, it was stated that there was no requirement that the degree be awarded, and one only needs to have completed two years of study after the age of 17 and using study permit.
On a positive note, you know for sure that at least the CIO considers the entirety of your 4 years or more of work experience (they assigned you 21 out of 21 points), so you won't have to worry much whether or not your work experience would be accepted, and that, with only 8 points for languages, and 0 adaptability point, you have 64 points already (which is impressive).
If you retake IELTS, and get better scores (at least 4 more points), then you know you'd get 68 points or 70 points (provided that everything else stays the same). My advice would be (if you have time obviously, and the financial means) to retake IELTS and try your best to get at least 12 points (or 14). I think if you do this as soon as possible, you can probably still make it before the cap is reached this year.
Good luck, and please do not give up just yet
For everybody else, we indeed now know that the CIO does more than just check the enrollment in PhD program and good academic standing. They actually DO check if you have enough points (at least according to their interpretation).