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Hmm. I couldn't reproduce this with the newest SDK tools on my Ubuntu 14.04 x86_64 machine (nor in a Docker image with Ubuntu 12.04), but it's strange that you get a different result on the command line.
In the command line version, are you running as the same user that Jenkins is running under?
Does the same happen if you run a Jenkins job, where you manually run the emulator command via a "Execute shell script" build step?
Is there anything weird in the build's environment, e.g. env variables injected globally in Jenkins (or on that particular build slave)? Probably you can see this by running env in an execute shell build step.