This is a known problem. In Transmit 3.6, we changed the layout of Transmit's Automator actions to address a number of issues. Unbeknownst to us, Automator saves an action's layout directly in the workflow, rather than asking the current version of Transmit for the current layout when the workflow is opened.
So, when you try to run your workflow with Transmit 3.6, it doesn't work, because its trying to use the layout from Transmit 3.5.6. Unfortunately, this usually means you are going to have to remove and re- add the Transmit-specific actions in your workflow. In the worst case, you may have to re-create your workflow from scratch.
We apologize for the trouble, and we are actively looking into safeguards we might be able to implement in the future so workflows will work across versions, even when the actions have been modified.