Possible npm 3 issue

[sagivf]

I have noticed a wired behaviour.

I published a simple module (lets call it "x") with one dependancy("bunyan") to my companies dedicated registry.
I installed it in a project.

If I publish a patch to "x" and run npm update on my project it updates but it installs bunyan inside the "x" node_modules and removes it from my projects node_modules which I need.
If i run npm install it reinstalls "bunyan" in the projects root node_modules but downgrades "x" to the previous version prior to the patch.
The solution seems to be: uninstall "x" and install again. then all is well.
Am I missing something?

[sagivf]

Is this in the correct repo?