Thunderbolt port 1 doesn’t work on my MacBookPro 2015

I have a MacBook Pro (Mid-2015). The logic board was replaced. Since then, the Thunderbolt port has the following issue:

The second Thunderbolt port works fine. I can use the official Thunderbolt-to-VGA adapter, Thunderbolt-to-Ethernet adapter and Thunderbolt-to-DVI adapter and it all works fine.

The fist Thunderbolt port however does not work at all. This happens in both MacOS and Windows Bootcamp.

If I boot into Windows, I can get a display from the first Thunderbolt port, but the image is cut off. The Ethernet does not work at all (The second port however works fine).

I took it back to the Apple store. They said they replaced an internal cable and test everything and it all works.

However, when I try it, it’s the same issue. The second Thunderbolt port works fine. However, the first port does not work.

Any ideas? Could it be a software issue.