There are many possible reasons for this sort of behaviour. In addition to running from a shell prompt as you have, it's worth looking for clues in your workspace log file, which is the file .metadata/.log under your workspace directory—the NPE that's coming up for you looks like it could have to do with the logging code itself, but the log may still help determine what was going on before the error.
Web searches for messages you find often yield suggestions for deleting various directories or files and starting again. I've sometimes been able to just remove parts of .metadata/.plugins/org.eclipse.ui.workbench/workbench.xml, though, for less destructive solutions.