So you still have a few possibilities. Usually we get a call from a friend of a friend after the window guy has been there a few times to re-caulk everything and says it isn't his problem.
Sometimes it is just his installation, but more often it is something more where the old window leaked for years or other problems start to show up just because things have changed a bit.
He, most times has done everything in his contract. What the contract never says is, we will remove everything down to framing and inspect for water damage and wait while other problems are fixed.
If I was called out to your house, I would inspect the roof for new nail holes that Oldog mentioned but with a low slope thats not likely. After that I look for the cheapest to fix distructive inspection I can do. That would be drywall around the windows above. I would be looking for rot and where it starts or if there is new water there( wet but no rot) I would also keep in mind that you have a very low slope roof and no visable venting in the soffet so this could be a very old ice dam problem and still what ever the problem might not show up inside the sheeting.