As a test, I created a new Jackpot query as follows:

mapclass java.util.Vector => java.util.ArrayList;
new java.util.Vector() => new java.util.ArrayList();

There is probably something wrong with it but I haven't worked out what yet as it is basically a copy/paste of the 
StringTokenizer => Scanner Query.

Every time I execute the new Query I get a NullPointerException.
Restarting the IDE made no difference.
I also tried:
mapclass java.util.Vector => java.util.ArrayList;
Which also throws an exception.
When: mapclass java.util.Vector => java.util.Vector;
Does not.

NOTE: The exception occurs whether or not there are matching occurrences in the source code being refactored.
I was using:
Vector myVector = new Vector();
Then commented it out for further testing.

Will attach message logs and source code as suggested.

Thanks.