I was attempting to install into trs with a route. But I dont see why that would make a difference as there are many routes built in. Trainz was not running the first time I tried the patch. Later attempts included trainz running.
I started by trying to go from 38017 to 40040 for the patch. What a disaster that was, content manager would only go about 1/4 of the way into reparing database then came up with errors and multiple screens telling me to register and saying I had invalid key number from the cd. played around for couple of hours, nothing worked so as it had never completed installing the patch. Had to find the file trainznativeinterface.dll and put that into the bin folder even before I could start trainz.
Then decided to go back and try the patch 38017 to 38285 and that one worked and I got trainz running again. So I am assuming there is a secret to installing the patch ,but for now will leave it as is.