Hi @AHK,
Thanks for providing those files! @colinbrislawn was able to confirm for me that you are in fact seeing weighted UniFrac distances greater than 1 (from the datasets you provided), so I wouldn't worry about any issues with those distance calculations or the output viz you were seeing on your end.
It is actually not unreasonable to see distances greater than 1 - @jwdebelius outlines the reasoning and mathematics behind why this can occur here, for your reference.
Hopefully this helps provide some clarification on your results!
Happy 
ing! 