This was an issue with the Application issue. We were able to prove this by opening the application in an RDP session or on the desktop and we saw the same behaviour.
Some standard applications such as Notepad save their last known window size and position on closure.
Similarly, some applications like CMD.exe will cascade the windows of each process.
The location of the app on startup is controlled by the application running in the server session and then the application position is reflected on the client. The window position is not manipulated by Citrix Virtual Apps.