If carz are disappearing at a spline point at a fixed road junction, this is due to the road being disconnected. Put in an extra spline point on the road just before the fixed intersection, delete the spline in between these two spline points, and reconnect the road.
Multiple undo operations have always been an issue and it's never, ever been good to do more than may three or four at a time. This is due to the memory buffer holding all this information, and the issue is compounded by the number of objects and the size of the routes. The good news is at least in TS12 this did not crash the program completely, however, spline objects, especially those attached to fixed objects, can get screwed with very badly. In TRS2004 through TS2010 it really was worse, there was that risk of losing everything with even a couple of undo operations. I got quite adept at doing things without resorting to the undo, or rarely using it and that has been the case even today.
The pits and peaks are related to texturing. If you look carefully, you will see that these follow along seams and sections. There is a finite limit to a given number of textures on a route, which today even in TS12 is far higher than it was in previous versions of Trainz. In TS12 the limit is 256 textures per baseboard. As textures are added, they will be added until they reach that limitation. When you've reached that limitation, other textures will fall off the stack to make room for the new ones. This can cause holes in the texture cover, which will cause holes in the mesh.
The color table in the game engine is made up of a specific number of usable colors by the user plus the greyscale textures used to represent height information. For user-generated textures, there is no true black, white or greys. These are reserved for heights with black representing the deepest, lowest point on a route or baseboard, and white representing the highest points. There's also a bug which is compounded by this, which has existed since the earliest UTC release back in 2001. When using the texture fill tool, the textures do not fill out completely to the edges, which causes black borders along the seams.
Starting with TRS2009, or thereabouts, the color-tables were changed to include the height information in the same table structure. This was an added advantage because it increased the total number of textures available to the user by freeing up memory space. This now causes the more obvious spikes in addition to the holes and chasms, which got worse as our routes have gotten larger and more complex. To add insult to injury, as we merge routes together, the color-tables need to be combined together as this then becomes a single route rather than two smaller, or large routes. In addition when this occurs, colors are dropped from the tables, and there are now holes and spikes. It's these black borders, remember black is the lowest point on the route or baseboard, becomes a hole or chasm. With the old black-border issue still there since UTC, we now have lines of chasms and sometimes spikes.
The problem, however, seems to have gone away finally in T:ANE, but is still apparent in TS12 perhaps due to the different underlying game engine and the increased amount of program memory available with the 64-bit program.
John