When creating the units, you have to use the standard units provided. In here you will see Tall, Base, Upper and Corner. So pick the correct type that your after, then delete all parts and work with the back HTH.
Another note is that if you select the tall pantry cabinet out of the standard list, it is considered a base cabinet. All base cabinets get mounted at the floor. The upper cabinets are mounted at a set distance from the top of the cabinet to the floor, which can be changed in "DEFINE STANDARD DIMENSIONS" (accessible in the Settings and Preferences, or by simply right clicking).
Just be careful when you take the cabinets into the countertop editor. The countertop editor has can take in ALL base cabinets, or just one or a group of cabinets by selecting them first; The tall pantry cabinet is a base cabinet. This will then allow you to stick a countertop on the cabinet. Unfortunately if it is joined up with another cabinet, it will stick it right through the middle of your pantry cabinet... Just make sure you don't select it when defining the outline of your countertop.