I've checked that the signal markers are clear of the switch sections so can eliminate that possibility. Wonder, perhaps, if the activity path is conflicting with itself somehow and throwing the signalling logic into a tizzy. I also wondered if you were trying to route the shunting operation in a manner that wasn't intended on the real thing as the signals placed in the YCR are as those shown on contemporary track plans. As I understand it, signals were set up to achieve protecting certain paths and other possible paths (but not regularly used) are not protected at all and required manual flagging should they be needed in exceptional circumstances.
Remember that the real thing did not have computer controlled signalling, it was down to the chaps in the signal boxes! So the situation running with computer signalling on a 1920ish rail network is somewhat contrived.
Other (non railway) computer issues I frequently encounter nowadays that never used to be a problem, ask for a particular product that you know is in stock in another branch of a supermarket down the road because you cannot find it... they say the computer doesn't allocate us any!!
Phone up a large company and try to find a real person to speak to. Sometimes virtually impossible (in more ways than one!)
Much of the real railway was simplified with sidings and crossings removed to allow computer controlled signalling along the whole line. So perhaps the only real solution to your signalling problem maybe to hire a real signalman to operate the Rillington box for you!!! How you'd install him in your PC though I'm uncertain.
I'm not at all sure MSTS was devised to have such complex routing and signalling as some routes have used. The default routes were somewhat simplified when compared to the real thing whereas the YCR was not so compromised. Perhaps we are fortunate that the signalling in MSTS generally operates as well as it does as the early reports of signalling in the new Rail Sim sound less encouraging so far from what I have read in that section of the forums here.
John
THE YORKSHIRE COAST RAILWAY, released as freeware (CD & download) on 26th Feb 2005.