I’ve found this solution by googling. I have just had this problem and it solved it.
My mistake was to put a project in other location out of the workspace, and share this workspace between several computers, where the paths differ. I learned that, when a project is out of workspace, its location is saved in workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/PROJECTNAME/.location
Deleting .location and reimporting the project into workspace solved the issue.