When you make a deposit through your QuickBooks desktop you should wait 5 minutes and check to make sure in your QuickBooks desktop that it has been accepted if it has not then it has been rejected.  Its just an extra step but it's worth it. It's important for you to update all of your emails with Intuit in all the appropriate places. They will say that that is your error because it's your responsibility. You can still ask that the fees be waived. It does not hurt to ask the IRS. Don't forget to log in to EFTPS every year and reset your password. 

If you are not a CPA and you have one they can do the letter for you asking for the fees to be abated.