When I originally started deleting rules 61 – 63, I saw the same results as you, rule 60 duplicated itself to 61-63. By deleting them all and then saving I managed to clear the entire QoS rules list. I then entered my 60 most important.
Its very true that the interface does not allow for easy creation of a large number of rules. It is certainly something I would like to see improved at some point, as I am currently using it to manage about 1000 clients (works very well).