Is the behavior specific to a given workspace? If you create a new, empty workspace with File-> Switch Workspace->Other…, and then provide a new directory name does this error still happen?
If the problem does not happen in the new workspace, what type of projects do you have in the original problem workspace? COBOL projects? COBOL JVM projects? How many COBOL programs are involved?
Once again, I'd like to confirm your exact product version. Please let me know what you see in Eclipse under Help->Micro Focus->Product Information.