I installed Pydev 1.5.3 (so that I could get the merged version of Pydev Extensions in core PyDev) in an EasyEclipse 1.3.1 installation. After this, Compare with > Base revision etc. comparison operations stopped working. I had to disable the PyDev 1.5.3 and revert back to the pre-installed Pydev 1.3.13 (part of EasyEclipse 1.3.1). 
Has anybody faced similar problem? Is there any work-around for this?