Have this problem in stable, and it exists in beta too. And I'm surprised that nobody has mentioned this in the comments yet, or at least I could not find it mentioned.

Case 1) When you have the train track in the games network menu selected, then open PRT and click the button to add "Same as selected", you get the identical train track but the name does not appear in the title field, and you cannot set the horizontal offset, it just ignores any offset you enter and places the tracks touching side by side.

Case 2) If you search for "Train Tracks" which is the name in the game's network menu, PRT does not find the network. The only non station track it finds is one called "Train Cargo Track", which is not the same network.

I say not the same network based on
A) the picker tool cannot find the "Train Cargo Track" when you click on a segment. True this may be a bug in the picker tool, but unlikely.
B) Every segment of the "Train Cargo Track" network is connected to the next one by a station crossover junction, i.e. the crisscross, which does not happen when you use the real "Train Tracks" network from the game's network menu.

To reproduce the first case
1) Open game's "Transport" menu
2) Select "Train"
3) Select "Train Tracks"
4) Open PRT
5) Click "Same as selected" plus button
6) Notice the network name is empty
7) Lay down two or more connected segments.
8) Notice the segments have a clean connection between each of them.

To reproduce the second case
1) Repeat steps (1) through (6) from the "first case".
2) Click the search button on the blank named new track.
3) Type in "Train Tracks"
4) Notice PRT finds nothing.
5) Notice the drop down box in the name field is empty.
6) Type in "Train" in the search field.
7) Notice PRT immediately adds the "Train cargo Track" network.
8) Lay down two or more connected segments.
9) Notice each segment is connected to the next by a crisscross junction, which is not what is expected.
10) Use the FindIt picker on any section of the "Train Cargo Track" you laid in (8).
11) Notice that FindIt cannot find the network.

Sorry that was long, but I hope it clearly described the problem.