As a test, I just built a new DB from scratch.
Added 2 locations
Added 1 siding to each location (one marked as yard)
Added 2 industries to each location (everything needing boxcars)
Added 5 boxcars
Created one train serving both locations, all industries.
Went into run trains, and you’re right, I can’t build a train, no cars found. Exited the program to load up the software in the debugger. Ran the program, and it works.
I think I have a handle on what the problem is. There is some startup processing that validates car locations. I should also run that when the Run Trains window is loaded. But try exiting the program and re-loading, see if that helps.