You might have risk been background checking.

My friend landed in Toronto, and went to apply for H1B visa. She got background checking and stuck in Toronto for one month. Eventually, she got visa, but she didn't plan ahead for the b/g checking. Luckly, her employer allowed her work remotely. So you have to prepare for b/g checking. IF you insist to apply H1 visa, be sure to tell the assistant that you are a landing immigrant, but not get your maple leaf card yet. Hopefully that will help you a bit.
Usually when you entered the room in Embassy (not in hall way), you will be asked to approach the 1st or 2nd windows. People behind the 1st and 2nd window are assistants. They will write down your reference # (the # you get from nvars.com when you made appointment), cross out your name to make sure you had appoinment that day, also they will write down your immigration status in Canada. Officer will look into your immigration status in Canada. Hopefully they will avoid your b/g checking when they know your Canadian immigrant.
Also, please be aware that Toronto Consulate General is implementing a new system. In the past, you'll get visa next day, but now It takes 5 business to get your visa even you won't go through b/g checking. So please plan ahead for this.