I'm assuming it will. Since I crossed after my first 6 month period of visitation they started bringing me in and asking me lots of questions and to show ties back in my hometown. It's all in the system, every time you cross. It only becomes a problem to cross multiple times for prolonged periods of time if you cannot prove any ties to the US. For example, owning property (a home, condo, etc.), a lease or rental agreement, a job, or any bills that you pay are proof enough to compel you back to your home town.
There's not a whole lot on this topic online either. I've searched to try and find some helpful advice, but with no luck. Unless you're specifically told to leave on or by a certain date, once a guard allows you into Canada, you have 6 months from the date you enter to leave. They may hassle you, and ask questions of why you were there longer than stated when crossing, but as long as you have ties back home and leave when you're supposed to, there shouldn't be major problems.