I seem to remember Scratchy having bottomless pit black holes appear due to missing textures, or something like that ... I never had this problem with TRS2006
If this is the bottomless pit issue, it's been known since at least 2010, which is what the OP has. Unfortunately, IIRC, N3V won't be issuing any more patches for that version.
Happened after I replaced the ballast texture over the whole route. I didn't notice until after I had done a good weeks worth of work....so either go back to my most recent backup or go back and fix every glitch, what a load of b.s.