Signals, that has specified "signal_groups=1" will show up as if the signal did not belong to any signalbox. I dont know if this is on purpose, in which case the .dat-file guide should be updated :)
This is known as it is marked in comments in mechanical-signalbox-intermediate.dat. I think that I have tried unsuccessfully to track this down; I suggest that you amend the documentation for the time being.
Thank you for your report, however.
Ok I see! I did not read that, so I have missed it. I will update the guide.
Thank you.