Sorry to hear that,
Unfortunately CIC officers are picky some times. It happened for me 2 years ago. I applied with the same letter which my friend applied. They approved him but rejected my application. Case by case is different.
One of my friends applied under 4012 code in April 2014. She had 3 years of work experience from back home as well. But her main code in the application was 4012 since she was PhD student. Her application got approved and she landed in 4 months (July 2014).
However, please check with others to see recommendation.
If I was in your shoe, I would apply again under PhD stream, but I would put my work experience from my home country in the envelope as well. In the cover letter, I would explain that work experience as well. Also I would modify the cover letter from the prof. There are some typical words, which MUST be in the cover letter, i.e. assists me in ..., full time work, paid work, responsibilities and ... .
Altogether, don't worry. You still have 1.5 month. But move on faster.
Good luck