Marvin windows leaking
It's amazing the ways water can find to get into a house. Could be flashing, could be somewhere in the roof (such as where roof meets chimney, or ????) The 'path of least resistance' taken by water can be more circuitous than one might think.
That said, there might be some flashing missing (or improperly installed) above the windows. Maybe when they installed the windows they took a 'short cut' and 'somehow' left off the flashing.
P.S., are the gutters clear? I've seen where flooded gutters overflow and cause water to cascade to areas that don't normally have problems--but if they aren't flashed (or caulked) properly the problem sure can appear in a hurry.
Water in the house is no fun at all. I hope you have an easy time figuring it out, good luck.
If the window is leaking, check the warranty and call the manufacturer. If the house is leaking, call the contractor. Most people will tell you it was installed wrong or flashed improperly, but I have living proof that these large window manufacturers are capable of supplying defective products. I hope this works for you, I had no luck fixing mine with Kolbe & Kolbe. They still leak and we are in a battle 2 years later. The only ones winning are the attorneys. If interested I have more information on my case at www.leakywindows.com