It might help if you would post pictures from on top of the roof so we can see the construction of the area where the roofs meet. It's possible that they relied on caulk rather than flashing at the junction.

If there is no flashing that is slid under the shingle sand overlapping the area where you tried the Flex seal(now you know why TV commercials are often fake), there will be leaks. Caulking will not seal that joint.

The fix could be something as simple as installing large drip edge flashing under the shingles and small screws driven through the aluminum into the vertical part of the metal that is there.

like this

I don't want to add to your trouble but that will quickly rot the facia,soffit and rafter tails leaving you with an expensive repair. That is one of the most common errors made by inexperienced remodel contractors. The usual remedy include's removing the cover to start over. The main problem is that cover can't be sloped enough so that water run's off without backing uphill and leaking between facia and cover. My solution for 90% of these is A, Remove cover while attempting to save as much material as possible. B. Add a gutter to house. C. Raise cover ABOVE roof on house or move cover away from roof of house. Leave room to replace shingles when time come's. If the mist coming between roof and cover when it rains bother's you, have a roofer install an apron in the gap.