I have a private repository to stash my node code and I tried to publish a module which was several months old and npm publish failed, details can be found in the following gist:
It looks like the issue is in publish.js, the loop at 126 (npm version 1.3.24) attempts to do an assignment from root to current, if the property does not exist on current the assignment fails. It looks like current is retrieved directly from the repository at line 98.
It seems that if this were an issue for the main npm repository it would be a big problem, but since there doesn't seem to be an outcry I'm guessing it's just with private repositories so possibly not a huge deal.
Closing as resolved – fixing this was one of the primary purposes of npm 1.4.