When new values are added to the Transpose By field within a Transpose node you must Get Values to add them to the rest of the down stream process of the job. This process is not done automatically do to the natures of the function of the node, and the amount of new values that could be created inadvertently.
When new values are included in the data, you must acknowledge that you want them turned into columns. To add new values within the Transpose Node: Click Values > Run to Get Values > Then make your selection of values by removing those that are unwanted.
Note: Holding down the shift button, you can select and delete multiple values at once.