I am having the same issue, the 2021 940 says Error - "Total of this column does not equal the exempt payments total. The difference is $248. You must make the necessary adjustments to reconcile the amounts."  see attached picture for reference... 

I have updated payroll and quickbooks so please no suggestions of doing that, it is already done. 

I am not sure where quickbooks is calculating the fringe benefits from, is there a way to see what is going into that number on the 940 line 4?