Should be absolutely fine. I've done this with totally unconnected flights before and no issues. You might get some questions about how you are crossing the border but the truth will be fine.
In the experience of my NA resident alien colleagues coming back in via the land border can be quite tedious so leave a good buffer. You will almost certainly get sent to secondary to have your I-94W processed (and pay USD6) and it can take some time. The agents can also be unused to non Canadians/USians other than at Niagara so you might get extra questions.