I run presta on a MTB with schrader drilled rims, no flat problems. I can see why there might be, but I think it is unlikely unless you have burrs or sharp edges on the valve hole (in which case, you should fix them regardless of your valve type).

My old road bike (27" wheels) has schrader valves on it, but I usually carry a presta tube. Makes it easier to help someone else out if I see a flat on a road (or if one of my friends is unprepared). I have not had a flat in a very long time on that bike, so I still have matching valves, but I imagine I will end up with mismatched valves eventually.