I had the same problem on my eclipse, and calling eclipse -clean did not solve the problem.
In the end I figured out that within the installation folder of eclipse there is a script called eclipse. This script does some setting of environment variables and then calls eclipse.bin. The call for eclipse.bin contained the command line switch
-data ~/.eclipse
When I removed that switch from start-up script, I got the workspace selection as expected. Maybe that helps others to solve their problems.