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I have found the problem. It is a bug in PyDev that is fixed in 2.5.0.2012040618
According to PyDev there is no way to update the plugins of Aptana Studio. So we are at their mercy to update it soon.
Latest Eclipse is using the latest PyDev mentioned above and it works fine.
UPDATE:
I have found the solution here: https://jira.appcelerator.org/browse/APSTUD-4759
It is indeed a bug in Aptana 3.1.1, which has been solved now in 3.1.2. I can confirm that this bug has now been solved in latest 3.1.2 stable version on Ubuntu 12.04
๐คHouman
Source:stackexchange.com