David,
Hopefully this is not being caused by the upgrade. This could be possible because the 941 pulls from the UPR00900 and the UPR30301 and the Employee Summary pulls from the UPR30301 alone.
You could also do a year-end close in a test company and compare the year-end wage file against the employee summary. When you find the incorrect employee then check the UPR30300 for the transaction.
- Most of the time it is due to manual checks and since the 941 report is date sensitive there be some voids or manual checks entered incorrectly or missing.
Run a select statement in SQL on the UPR30200 and check for manual checks that did not include EFICAM or EFICASS.
Hope this helps,