Try saving the file without it automatically being place into the track file. If it works, you will have to manually position and size the object in the track file. I have come across this problem several times in the past, and that was the only way I could get it to go away. Getting the object to fit correctly afterward is a bit of a pain.
^ You don't have to move/size the object manually, just set the editor's importing to disable auto scale and auto center.
Having it automatically placed in the track file could lead to problems anyway since the Tunnel Maker was made quite a while back. You will likely lose basics like environment references and support beam colors but I wouldn't be surprised if the subscript out of range error is also being caused by this.
Unfortunately, there may be a catch to that. NL's 3ds placement has been very temperamental for me and last time I tried to place a station I modeled by using a CK 3ds export as reference, the object placed in NL went glitchy; the placement node would usually not appear. Otherwise, you'd normally put the placement node at the very center of NL'd coordinate system, the origin, and it should line up. I ended up having to enable auto-center and placing the object manually, but at the very least I didn't have to size it manually.