While I was involved with the C&TS in 2000 and 2001, the answer is no. Don't know about the rest of the time.
It would be interesting to hear from Earl or Carlos how frequent the close calls are. Earl has mentioned it on at least one occasion.
The enginemen probably approach the crossings with a great deal of caution, but if it is a heavy train that the engine or engines are straining to keep moving, there must be some reluctance to back off on the throttle. This would be expecially true of the second and third crossing.
There are probably three reasons it has not been pursued. One it costs money, since the programs probably don't pay all the costs, and there has been a chronic shortage of funds (and other problems). Two, so far as I know none of the regulatory agencies have raised the issue. And three there is probably a bit of a bias in favor of keeping the bucolic flavor of the line. Of course the fourth reason, the fact their hasn't been a collison yet is not a good one.
My preference would be to use flagmen on a regular basis. But it would be interesting to hear what the folks actually running the trains think.
JBW