Agree with these guys. Make sure your flashing laps under the shingles (bottom row should be doubled to address keyway issue) by at least 6-8". If you have exposed keyways, then measure from that point. Another common source of leaks I've seen is a byproduct of the installation process (for some contractors). With most pitched roofs you will see them nailing 2x4s or similar (through the shingles) as footholds during installation. This is pretty common, but I would never let someone do this on my house. Some contractors are good about sealing the holes at the end of the job, and this is better than not. If the damage is done, a good sealant at each penetration is the only way to fix it.