Here's a better illustration of what I think was the problem (at least, cleaning up my layout to remove this track configuration fixed it): https://www.dropbox.com/s/2midtn6gtvkpdui/NoReallyWhyIsThisSignalGreen.zip?dl=0

http://i.imgur.com/MFGgdL4.jpg

The northeast-bound signal here definitely ...

Oh, it's definitely a mess . But messiness notwithstanding, if there is a train (or 3!) on the block, the signal leading to that block definitely shouldn't be green.

Take a look at this savegame: https://www.dropbox.com/s/560nfi9xs4qnk2d/WhyIsThisSignalGreen.zip?dl=0

The northbound signal I'm standing by is green, but there is a train sitting on the tracks to the north. Why is this signal green instead of red?

I have tried deconstructing and reconstructing the ...