I am having the same issue.  Quickbooks has it set for 1% for EACH company and employee for a total of 2%.  There is no way to edit this so that when I run my quarterly reports, it says I owe more than what I really do on paper.

Also, it is not calculating properly on the employee pay stub even though I have the correct percentage showing under each employee in the other taxes tab.  I am having to manually calculate the .6% (60% of 1%) on each paystub and make adjustments.