Dynamo alters direct input at will?!

[pyXam]

There is a possibility from what you are describing that element binding could be your issue.
Jacobs post below re: this.

Element Binding in Revit

Element binding is the name given to the process which Dynamo manage to ‘track’ the items created in non-Dynamo files. In this case, I’m going to focus entirely on element binding as it refers to Dynamo for Revit, but the mechanism exists to allow for this behavior in other applications (advanced steel, fusion, alias, etc.) as well. In the context of Revit, ‘elements’ refers to anything with an Element ID in the Revit database. When utilized correctly, element binding will expand how you leverag…

There are methods on the forums for removing element binding, the easiest being, copy your whole graph and paste it into a blank document. Save it before you run it and don’t save it after that.