Is this occurring on a home (interlocking) signal or a distant? I use these and his NORAC CLs extensively and have not had problems; the only bugginess I know of concern end-of-siding situations and AFAIK those only affect the position-light signals. I also know that mis-setting switch positions with home signals can really mess things up.
You do need to set a distant signal for every route unless a route is unsignalled (or signalled only in the opposite direction.) GrahamSea signals do properly handle combo signal aspects, such as medium approach medium.
Tip of the month: Avoid buying Trainz on Steam, especially if you intend to gift it. Apart from the game differences, Steam keys are not the same as CD keys and will not work!