My wife and I have had 4 TREK bikes and a Raleigh. On every one of them I have routinely taken a small round stone to the valve stem holes in the rims. I have had to fix flats where the rubber around the valve stem was cut through by the edge of the stem hole in the rim. A few had burrs left from the drilling of the hole while they all had sharp edges around the holes. The round stone was used, by hand, to remove the sharp 90 degree edge of the holes. This is just a fact of life with the budget priced rims found on most of the lower priced bikes. Once the edges are rounded it should be the end of the stem rubber cutting.