I can confirm this behaviour.
Working on a Mac, using subl, I can create a project. I save the project file within the same folder (project folder).
When calling the project via ‘subl projectname.sublime-project’ or ‘subl --project projectname.sublime-project’ Sublime will open with the project, come up at the same time with the error message ‘Unable to read project …’. When I confirm the error message it comes back a second time with the same error message, and after confirming the second error message it will close Sublime.
While sublime is open and the error message not yet confirmed I can see the project open in Sublime.
I have the same issue on Ubuntu, just there Sublime does not close when confirming the error message.