It appears there is a bug in the experimental 'Enable fast rerun' option. If you turn this off, you should be able to commit without exceptions again.
Edit: Fixed in Mendix 5.4.1, see https://forum.mendix.com/questions/6131/Mendix-release-announcements-and-notes-in-here-most-recent-541-483
Paul, This seems to be a big bug/issue with 5.4.0, a colleague of mine is experiencing the same issues only on windows 7. Did you already filled in a bug report?