I am not a tech guy but this is what I have encountered in figuring out how to use Non-Stackable counter is Vassal. The rules could be different with other modules. If you have better information please hold forth.
For manipulating Minefields, Factories, City Control Flags, and Railway Conversion Markers:
1. The first thing you may have to do is UPDATE 1st JAVA and 2nd VASSAL to the most recent edition. JAVA must be updated before VASSAL. If you already have the most recent update of VASSAL, uninstall it, 1st update JAVA and 2nd load the most recent copy of VASSAL. I am now using JAVA 8 update 111 (just updated to solve this problem) I am using VASSAL 3.2.16.
Let me give you some links. After I'll explain how to manipulate rail markers in VASSAL. (Note: these links date from late 2016 they are time sensitive)
In the US for Windows 8 or 8.1 this is the webpage to see what version of JAVA you have and how to update it. https://java.com/en/download/installed8.jsp
Windows 10 supports Java though it doesn't function with its new dedicated browser. https://www.java.com/en/download/help/windows_manual_downloa...
If you have an earlier version of Windows you may not need the latest version of JAVA but you probably need the highest update possible for your version of Windows. I think Windows 7 still uses JAVA 8 update 111.
If you use Apple or something else, I'm afraid I can't help.
2. VASSAL Functions with markers. (2nd button over from the die- it looks like a unit with a "2" marker place on it)
Rail Markers, city control flags, Factories, Minefields are all what are called Non-Stackable Counters. It is done this way so they do not join a stack that moves through the hex.
Non stack-able counters have to be selected by Shift + left-click. Then let go of the shift key and you can left-click on the selected game piece and move it around the map or to an open storage box, etc. Also, you can: right-click and a drop list of functions will appear that you can select from with a left-click.