They don't call but write letters to all your former places of employment and schools to confirm that what you said in your application is true. Calling would be too expensive and inefficient. If the source is slow in writing back, that could be the delay. Additionally, seperate security background checks are made on you, and they also have to contact various law enforcment sources (depending on where you're from) to make sure you have no criminal background. This also could be the reason for the bit of delay.
I wouldn't be too worried if you left any prior employer on not the best of terms. Canada just wants to make sure you worked where you did, for the amount of time, and in the position you stated in your application.
By the way, I also have MS degree (computer scienvce) and worked in IT. The MS degree gave you some additional good points in your application.