mongod instance should not cause this kind of problem. Despite running the shell and
mongod on multiple VMs I have never seen this behavior, hence I can't really suggest what might be causing it.
As a general recommendation, I would not use 2.0.4, it is well over a year old, and has been superseded by 5 minor versions in the 2.0 branch (as of writing this) and by 2 major versions (2.2 and 2.4). Hence, you might be running into an old bug that I am not remembering. At the very least I would recommend getting hold of 2.0.9 and preferably using 2.4.4+