Hello Andrea,
I have a client that is using QB Ent 20 and had the same issue - it only affected one employee starting with their 8/31 payroll but it was only the employee medicare that was doubling and I caught the error when preparing their Q3 941.
I found a "work around" that fixed it so that the taxes would calculate correctly (after spending hours trying everything you have tried).
Here's what worked for me. I made the employee exempt for medicare taxes and then proceeded to correct the old paychecks removing all the amounts withheld for medicare (the incorrect ones) into a "clearing" payroll item that I labeled tax adjustment. Then on the last paycheck, I let QB calculate the crazy wrong medicare tax amount (even though the employee was labeled as exempt) and plugged the difference to that tax adjustment account.
I then made the employee subject to medicare tax again and when I ran a dummy payroll, it seemed to fix it. So, I think what you might need to do is let QB override the medicare with the amount it wants to calculate (even though you know this is wrong) and then make an adjustment to add back to the employee's net pay the amount over-withheld. At least this way the medicare amount will be correct on payrolls going forward.
I'm sure this will need to be a manual override when you prepare the Q4 941 and W-2s, but at least the payrolls from here on out should be correct.
