Did you remove everything from the track? Maybe in your quick shut down, a car came off the track with the sudden stop? edit: I suspect you didn't remove stuff from the tracks, otherwise you would not get different "off" readings connected vs. not. The lighted cars or engine can provide enough of a load to drop the very low voltage without actually moving or showing a lot of light.
Is it possibly you have something like an operating track included with your accessories, thereby creating an opportunity that a derailed car could be connecting the track hot to the accessory hot?
Did you measure B at the back of the transformer with the original condition? You say you disconnected everything and got nothing more than low readings that could be normal when "off". Did you try to raise the handles to see what measurements you got? It seems to be something in the layout wiring, or what is on the track. I can't see the problem "following you" from post C to post B if that short is not present with no wiring as well. edit: I re-read and see you didn't say anything about raising the handles when the track was disconnected. My stricken-out thoughts were assuming you had done it that way.
If you remove everything from the track, you should get those same phantom readings when the transformer is hooked up to the track, unless something in the layout wiring (between transformer and track) got fried. edit: again, the phantom reading terminology seems to suggest you did this with handles off. did you raise them to see what voltage behavior happened without being connected to the track?
If stuff is still on the track, removing it all is job 1 in figuring this out.
-Dave
