I disagree, a taught MSc and a research one are different degrees, and it does make a difference - that's almost like saying there isn't a difference between the exam and research side of a PhD!
To elaborate - if you are given a choice between two students:
- one has a taught MSc with some relevant courses and a minor project that isn't particularly relevant,
- the other has a research MSc whose thesis was on a topic very close to the proposed PhD topic,
it's pretty clear that the research MSc would have an advantage.
However, don't see this as a discouragement! I don't know much about the exact admittance policies in USA/Canada, but what I've found to be an important admission criteria in general is that the student demonstrates a clear understanding of and interest in the proposed PhD topic.
This can come in the form of good grades in relevant courses and/or research experience. I would imagine that if you got fairly good marks in relevant courses and your research project is relevant to the program that you're applying for, then you'd be in with a good chance. Just be aware if you do mediocre in your exams and work on a project that has little to do with any of the profs' expertise in the program then you are lowering your probability of admittance.