Thank you both for your replies.
@MoiraGoggin, so far, we have not pinned it to a suspect employee. We thought we had but it is intermittent and on a previous payroll that had the issue, the suspect was not the cause. I have not run in a test company because it doesn't happen all the time.
When this first happened, I found that PR9 and PRA each had a record when the files should have been empty. I re-initialized PR 6-A and the next payroll worked. This time I found the same thing so I deleted PR6-A and re-initialized them manually. Then I rebuilt keys for all PR files and the sort files. Not sure if that is related or not. We will see.
The payroll is not imported.
@DebbieBeach, I went through all 36 pages myself . :) All deductions are either set to All periods or None. Because they don't use the periods, I would bet the period is just the default every time. I brought that up but because they regularly have employees off a week or so, they handle deductions that only occur a couple times a month manually.