I get the error as well (Eclipse 3.4 64-bit, PyDev 1.3.20). After
repeating the error 17 times, I've found that there are 3 different
compile tasks where this will occur. In addition to the
PythonPathHelper.isValidSourceFile that Thomas and Servilio reported,
I've also found:

C2:780  !
org.python.pydev.editor.codecompletion.revisited.PythonPathHelper.resolveModule(Ljava/lang/String;Z)Ljava/lang/String;
(670 bytes)


C2:422      
org.eclipse.core.internal.dtree.DataTreeNode.forwardDeltaWith([Lorg/eclipse/core/internal/dtree/AbstractDataTreeNode;[Lorg/eclipse/core/internal/dtree/AbstractDataTreeNode;Lorg/eclipse/core/internal/dtree/IComparator;)[Lorg/eclipse/core/internal/dtree/AbstractDataTreeNode;
 (469 bytes)

-- 
VM crashes while PyDev scans the system Python libraries
https://bugs.launchpad.net/bugs/258088
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