I am also having the same problem.  Not with every employee that I am updating but most of them.  Called support and was told that they don't have any answers.  

My process:

Go to W2's and click on Edit Box 12/13 

This brings up all employees that we have ever had (so yes it lists employees that were terminated 2 or 3 years ago) ALSO not in alphabetical order!!!  Can only load 10 employees at a time - again not in alphabetical order.  We have a total of 625 employees that are in QB so I have to load 10 employees at a time and search to find the person I need to update.  Once I find the person I enter the $ amount for Box 12DD and hit Submit. 

Go to the W2's and the amount that I entered is not on the W2. 

I have over 100 that I need to update Box 12.  Quickbooks has no answers as to why this won't work. 

Also when viewing my W2's I get an error and they said to print 20-30 at a time so I don't get errors printing the forms.