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I think the issue you are describing really stems from poor semantic versioning. People will peg to specific revisions that they happen to use rather than depending on the general major or minor revision level, so small fixes don't naturally propagate to second- or third-level dependencies. There's no good solution to the problem that doesn't lead to other sorts of hell (imagine asking users to manage the revisions for third-level dependencies)

Were you using Windows? Although node.js "works" on Windows, there are a number of modules that only compile under UNIX, which makes Windows basically useless for node development.

Might be worth your while to give it another shot. Npm is so lovely.