First as Jeff said
http://groupyahoo.com/group/waterjets/ is the best place to look.
Personally I am not a fan of Flows software to run their machines. I think it limits the operator too much. I would prefer G& M code any day.
For your problem
Is the problem worse on the bottom or only noticeable on the bottom?
Do you have an option not to have a lead out and still use a lead in?
Do you have different options for lead in/out (like arc)?