Hi Guys,
Just to let you know, Asad and I had the same problem i.e our visa was issued for 18 months while course of study is 2 years. I spoke the immigration officer at Toronto airport and he issued me study permit for full length of my course. So if any of you faces the same problem, just mention it to the immigration officer at the PoE and surely they will issue you study permit for the full length or your course regardless of visa duration.
Cheers ;-)