Do you know that you Lotus recommend that when you upgrade using the QMR's, you should at some point perform an uninstall and re-install to clear out all of the miscellaneous files. Normally this is done at point releases (5.0.5, 5.0.6 etc), so if you incrementally upgrade from 5.0.2 - 5.0.5, either 5.0.5 or 5.0.6 should be a fresh install (copying all nsf, id, dsk and modified templates over the top of the new install).
McElvis