The Train Holding Tracks are a bit non-intuitive. It appears that the rail will remain "on" for an arbitrary amount of time after the red-stone signal has been removed. Two potential solutions come to mind that may help make the track more useful:

1. Allow for an adjustable delay (whack it with a crowbar, pick a delay with a GUI similar to the signal capacitor).

2. (preferred) Be more intelligent about the time the track stays on; As soon as the end of the train exits the block space, and the red-stone signal has been removed turn off the track.

I think that the 2º solution is more intuitive and more useful. You can do "1" with a "State Cell" (Proyect Red) and a normal "Holding Track".

Updated the original post to emphasis that the second suggestion would be preferred, just listed the first as it may be simpler to implement.

I'm aware that with the help of another mod, or some creative vanilla redstone I could make the standard holding track work for a train, but that sort-of defeats the purpose of the train holding track.

I'm not sure I understand what exactly you find unintuitive about them. Yes, they stay lit for like half a second after activation, but why is this a problem?

And if you are not talking about the latest version, well the 1.6.4 versions were bugged and broken.

My issue was that If I power a single holding track for 1 tick, it will let exactly one cart through no mater how close the next cart is. If I power a single train holding track for 1 tick, it might let through more than one train if they are close together or moving fast.

I see though that version 9 has changed this into a holding rail with different modes, which seems to act as expected. Apologies for not testing with the newest version before posting an issue.

Yeah, that was a bug.