Currently the MDLV2000Reader uses IBond.Order.UNSET for bonds of order 4. This renders atom typing for the atoms of the UNSET bonds impossible because the maximum bond order will always exceed the theoretical pi bond count of the atom type (CDKAtomTypeMatcher 2544). This is a result of the ordinal() method used (container.getMaximumBondOrder(atom).ordinal()). The ordinal of UNSET is 4, greater than most pi bond counts of most common atom types.
In turn that means that all subsequent methods which rely on typed atoms fail, such as the FixBondOrderTool (which could be used to get around the issue of bond order 4).
One way around the problem is not to use ordinal. John has posted an alternative approach for 1.4.x (https://sourceforge.net/p/cdk/patches/569/). Adding a custom connections method to the enum would replace ordinal method calls and could return a lower value.