Maybe bug. I create an entrance to the tunnel, switch to underground mode, but I couldn't build it track with help tunnel tool.
Forgive my ignorance if this is not the case, usually play Britain. Is the tunnel and the tile ahead of it both a full tile depth? I had similar problems until I realized I was trying to build full height tunnels in half height blocks, like as in raise/lower tool only does half a "level" at a time.