I have this weird issue where the following happens:
I solved this problem as per JJ-za's answer, except steps 2 and 3:
In {eclipse_dir}/configuration/.settings open the file org.eclipse.ui.ide.prefs (when Eclipse is not running)
Find the line
RECENT_WORKSPACES=and confirm that the workspace is pointing to the correct workspace directory and that multiple workspaces are separated by\n