I'm a Canadian (F-1 visa) graduating from an American Medical school who just match in an academic medical center in a major metropolitan area.
First, we (i.e. Canadians) are in a VERY unique situation, since were are not FMGs; however, as IMGs, we come from a country with a unique relationship with the US. Certain rules/visa apply to us in a different manner than someone from a non-Canadian country.
The Canadian citizenship issue is a nebulous subject for every single person I have asked...it should not affect your application, but it may affect how a program ultimately ranks you. This is really based on personal experience and not on any hard data.
Regardless if you have graduated from an American Medical School, some research-intensive schools may have worries about your ability to apply for research grants (as a non-American). Others may only give out J-1 visas (the one where you have to leave the country for 2 years).
Please be aware that you need to be extremely vigilant with follow-up on programs...some may inadvertently delete your file because they assume, as an F-1 or a non-US citizen, you are an FMG. Obviously you are not!
Contact me directly if you'd like to discuss this more.