Yes, if you are pitching most of the time flat, then that is the problem. Your timing will get screwed to hell if you make that jump without practice. A major league mound declines one inch for every foot, so if your stride is 6 feet, your end up 6 inches lower than where you started. Convert that statistic to someone who has had their foot landing on the same level as he started, and you have a problem. Basically, your body is ready to throw, but you still have another 5 or 6 inches to drop, which will cause you to throw a flat fastball and be all over the place.
Work to reestablish yourself off the mound before you pitch live again. Try and take everything slow, so that your arm is not in throwing positiong while you are still in the midst of striding. It will take 3 or 4 bullpen sessions before you are at the same level you were off flat ground, but at that point you will probably see benefits of extra speed on your fastball, and more downward action on all your other pitches.