Hello,
I've tested this out two ways:
First I took the New Rochelle - Stamford route in QD (Non-MNR).
I encountered the same problem as you did - just after Old Greenwich Station I got a "S" signal at the West Stam. Interlocking and the signal speed was set to 0. I was able to get moving once the train had stopped and after I turned the ATC off.
I'm not sure if this is the same exact route you took, but I found out that the reason for this is because the QD randomly lines you for the Stamford yard, so it must be throwing a stop signal of some sort (Shouldn't it be restricting?). Here's a picture:
20160621201541_1.jpg
Next I tried the Old Greenwich (MNR) - Stamford (MNR) route in QD.
Same exact thing happend, except I got a "M" signal right after leaving Old Greenwich. The path was lined into the yard again.
I tried it another time but with trying to get permission to pass signal at danger by pressing TAB, but that didn't change the signal indication.
So for now my solution is just to turn off the ATC by pressing Ctrl-D (stated in page 8 of the M8 Manual) right before you get to that interlocking. If it goes off, just press Q when the train stops and then you'll be able to proceed after turning off the ATC. I'm not sure what else to do, but maybe there's a way to modify the QD?
EDIT: If you're taking the MNR route, just set the quick drive end to Noroton Heights but stop once you get to Stamford. You'll get an "N" signal (normal) after passing the West Stam interlocking, and that kind of "fixes" the issue.
Hope that's helpful.
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