Project Setup Station gets stuck (not responding) in the middle of the project upload to the application server.
It is quite a common thing when the Project Setup Station freezes while uploading/exporting a project to/from the server especially when the project size is not small.
It is ok to leave it frozen, as it usually unfreezes itself. There is no need to close it forcibly, just let it finish the operation.
Optionally, it is possible to upload/export projects using FlexiCapture Admin Tools which are run in the command line, so it is not required to use Project Setup Station for those operations.