I don't have your flatcars. I used UP 50' Flatcar which has a built in load of the 40' logstacks. One of the problems with the logstack industries is that the quantities are very limited. Nevertheless with careful timing I got a one car train to unload and the other one car train to load on their respective tracks.
An alternative solution* it to attach invisible track to the logstack industry. Then place a Multiple Industries (regular or short) Object in front of the logstack. This solves a lot of problems (for me). For one, you can now enter on a straight section of track if you want to. The other -big- improvement is that you can have a lot logstacks in inventory and load up even a very long train. It also gives you the capability to just have one track going to the industry for loading some trains and unloading others. Using dual gauge track, you can deliver from the woods on narrow gauge and pick up on the same track with your standard gauge trains.
You do lose the visual of the amount of logs in your stack changing, but you will see the cars filling and emptying.
* I used this technique with the Dry Sort Log. I lost some of the visual effects, but gained flexibility.
