Writing from memory as the testbox is down at the moment. I think this happened "inside" the beta3 system, ie. I was force-upgrading setup from beta3 to setup from beta3. 1) Modify some files in /etc/ a little, like profile or bashrc 2) Check that they're changed by rpm -V 3) Upgrade the respective RPM. 4) Notice that that file was _not_ upgraded (even though it was significantly changed). Also .rpm{save, orig} was not created either. Effectively, changes in the file were lost. The only way to get around that was to delete the file, and then upgrade.
This is a feature, not a bug in rpm. For config files, if the attributes (MD5 sum, mode, perms, etc) of a file from a new package are identical to the old package, then a modified local copy of the file on disk is not changed, nor are *.rpmnew and *.rpmorig files created.