RDP is not recommended as a virtualisation tool for a number of reasons, one of which is the problem you are facing. RDP requires that the RDP window remains open and in focus for the duration of the process. If you close or minimise the window then some operations attempted by the process, such as mouse clicks and keystrokes, will not succeed. This is why parts of the process seem to work and other do not.
Search this forum for RDP to see similar discussions, and for an overview see
https://portal.blueprism.com/system/files/product/productpublic/5.0/Blu…
For more details please contact your in-house BP Architect, your 3rd party Architect, or your BP representative.