Local immigration is a DAMN PAIN! My friend, who also came with me, was harassed so much because he was traveling for the 1st time (show this show that where were you born blah blah) but he was able to pass smoothly through the POE!
Well now that you have the deferral letter, just go through the immigration and if the officer tells you any further bull___, just file a case against him (I am pretty sure that India is very strict about these things) because you have the right to go to Canada now that you have both your deferral letter and visa.
At the POE, they might ask you why didn't you catch the earlier semester, just be honest with them.
About the visa, we all get visa less that our course period. It is their policy I guess. So just before 2months of the expiry date, you have to apply for the permit online and voila you are done