I don't do Skype, but I have a couple of questions. How much does it slow down and for how long? Is this an AI train or are you driving? I have noticed (though I've never really tested it) that an AI train sometimes seems to slow down after a "Navigate/Drive Via" command. It doesn't actually stop, but seems to coast as if it went from drive to neutral. I "think" this is because AI trying to verify that all the junctions are set correctly, no other trains are on the track, etc. before it executes the next command. As I said, I've never really tested this and if I'm wrong I hope someone with more understanding will correct me.
"It's never too late to have a happy childhood." - Tom Robbins