Please check on the latest PyDev 2.6.0 release (there was an issue
related PYTHONPATH ordering inside PyDev which could potentially lead
to that).
If it doesn't solve it for you, check if your PYTHONPATH is what you
expected inside the shell: import sys;
print('\n'.join(sorted(sys.path))) and compare that with your
configuration... ( note that the recommended place to ask PyDev
questions is at stackoverflow with a PyDev tag... see:
http://pydev.org/about.html )
Cheers,
Fabio