MacCraigus: Hi!
Did you have a look at the station tracks?
By default the stations are built with standard speed/non electric lines, unless you change their options before building.
This catches me out from time to time as the station defaults are reset each time the game is started/loaded.
Easiest way to fix is just use the track update tool to highlight what section is non-electric.
Abwig: Yes I had already update the tracks.
The strange thing is the signals work ok on goods trains, but on passenger tracks the trains just ignore the signals, it is strange.
Yeah, it would be too easy, but it pays to begin with hoping its something simple!
The only other things that come to mind are:
1) somewhere in your new line there is some
passing track that has normal track, hence why its only showing up intermittently (ie whenever trains pass eachother).
2) sometimes when a track is in a tunnel its hard to tell if its upgraded or not.
3) I have had it where the most impossibly small segment of track has been formed and it isnt easy to see unless I zoom in a lot. Usually the result of a lot of track 'editing'. This has led to difficulties in upgrading the track. I find zooming in and using the track speed tool to be the best method to find these small segments.
But in your last sentance you alude to a signal problem? I don't see how a signal can tell a passenger from a freight train. Maybe a mod causing the problem?