Hi costas
I think you're facing a rounding problem!
Even you're thinking the boundary nodes are the same, if you select the same node on both mesh, you will see that the coordinates are differents.
In such case, the merge cannot work properly which explain the creation of a boundary condition inside your model as in fact, th mesh are not connected!
I didn't try but you probably have to make a shift in your model to avoid the roundig problem. As i see, it seems this is the boundary of the submesh which is rounded at 10-1.
Hope this helps
to illustrate, I join two screenshots