Sorry I did not post the solution for the problem.
The client and I invested a huge number of hours looking at the data, looking at the reports and trying to determine what was causing the problem.
We eliminated the data as a problem as we were able to get a Smartlist dump of the Profit and Loss accounts and got to match a number we were seeing on the reports. That was the Balance Sheet value. So then we knew that the problem was on the Income Statement.
Focused on the report and we tearing the report apart line by line. Looking for missing accounts.
There were no missing accounts.
What we did not look so closely at was the filters on the columns - bottom line determined that the issue was a filter on the column that did not include one of the department values unless the Roll Up was done a certain way.
Once we removed the filter all was corrected and the values on the reports all agreed.
Thanks to everyone for your time and effort in looking into this matter.