I had this same issue. I thought it was flashing too. The leak was in the garage along the shared wall with entry way. It leaked out at the wall and garage ceiling, no visible damage to the ceiling. I thought my warranty had expired so I ran a bead of asphalt caulk along the flashing. It was a rare occurrence for it to leak. Heavy winds were the common denomintaor, so in 5 years it leaked about 5 times. Once I realized the caulk didnt fix it, i rechecked my warranty and saw infrastructure issues were still covered. Warranty roofer came out. The original roofer, very good reputation for quality of work, so he told me
. He was mad to even be there. Went back to the warranty office and had them void my entire roof warranty. I thought well thats absurd, a bead of caulk? I went and got estimates, and every roofer I talked to said the same thing. $2800, very common problem with raised entryways. I raised a stink with warranty. My justification was the estimates, common issue and I did have signs of a repaired ceiling on the other side, but in the entryway. After quite some time, I was able to convince the developer and the same roofer to come out, they ran water for quite a while on every part of that juncture they could think of and could not find the source of the leak. They were in the attic with flashlights. Couldn't find anything. We were talking on the porch and the developer thought of something, we then all went over to a neighbors looked at the roof and confirmed the problem was most likely the vented soffit on the the raised roof. The neighbors was solid, no vents. I had vented soffits. The wind would blow water off the main roof, hit the sidewall and blow it into the vent. So far I have not seen a leak after they replaced the soffit under warranty. But I have not seen very high winds either. So check the roof over your entry way on the sides, vented soffits are bad (supposedly). Should be a warranty issue. The front vented soffit is OK. Good luck!