You need to uncheck the "copy projects into workspace" checkbox, and after that click "refresh" button, you will be able to import your project.
In my case, I just copied one of my projects (say 'Project1') from a workspace and pasted it to a same workspace. After that I modified a name of a pasted project (say to 'Project2'). I could not see it in a repository.
A main reason was .project file from a new project still had a: <name>Project1</name> instead of <name>Project2</name>.
So, I did below things in order to get my issue fixed:
- Cut and paste my Project2 outside my workspace
- Changed my .project file to have <name>Project2</name>
- Tried importing my Project2 again.
It simply worked for me.
Maybe you get a same project name in the '.project' file, just check it again, if yes, then simply rename another name. and import again.