Well... Now it gets really weird:
The problem is solved! Point is I'm not sure why..
I changed the position of the decal again. Then I started the scenario and part of my tracks were gone in the area of the tunnel! I was afraid I accidentally deleted tracks while fiddling with the tunnel...
So I opened the editor and took a look. The tracks weren't visible but the trackmarkers were still there! So I didn't delete them, they were just invisible (like the tunnel decal!!!).
I restarted TS and went into the scenario again. Now the tracks were back (visible) again and: The decal works!!! More amazingly the other problemdecal, on the other side of the track, ALSO WORKS!!!
.... uhm... 
So my guess is it all has something to do with the build up of the route when starting. Maybe the sequence in some bin file influences it. Which means it is really hard to repair but editing/rebuilding the problem area (portal/terrain hight/decal) might just re-shuffle something and solve the problem..
As we all know: what you see in the editor is not always what you see in the scenario when you restart.. which can be a real pain in the ass 
Hope this helps (a bit), don't give up!