Just a bit of an update, I forgot to add signals are each station I think its solved that issue, but I guess it might still just be down to timing. Attached is an image of what I have done.

Hey,

I have attached an image of what I have for my dual train system, for those that might have play transport tycoon it is an idea taken from that.
However every now and then they do what is shown in the image, anyone got an idea to make this better?