That is because in the second case, the actual date objects are compared, and two objects are never equal to each other. Coerce them to number:
alert( +startDate2 == +startDate3 ); // true
If you want a more explicity conversion to number, use either:
alert( startDate2.getTime() == startDate3.getTime() ); // true
or
alert( Number(startDate2) == Number(startDate3) ); // true
Oh, a reference to the spec: ยง11.9.3 The Abstract Equality Comparison Algorithm which basically says when comparing objects, obj1 == obj2
is true only if they refer to the same object, otherwise the result is false.