You need to define a custom command encoder to be able to translate your trait to and from the string that is stored in your saved module. Tim has a very good, basic example in the forums here:
https://forum.vassalengine.org/t/programming-tutorial-mycounterfactory-class/4627/1
What’s happening right now is that the basic command encoder is trying to parse your encoded custom trait, not finding a matching basic trait, then giving up and making it a Marker. Check around line 303 here:
vassalengine.svn.sourceforge.net … iew=markup
I bet you’re also getting an ‘Unknown type’ error in your chat window.
-Seth