Unfortunately, I'm seeing a similar issue after upgrading from Tableau Server 9.2 to 10. I have a workbook with groups in it, and it refreshes correctly in Tableau Desktop 10.
After I publish the workbook, it renders correctly in Tableau Server 10 until I have the server refresh the extract. Then I get the same error message as you:
Tableau Data Engine Error: 40401: Scan::Next: Mismatched row counts: Table has 597485 rows: Column: [PositionSubLoc (group)] has 0 rows
I contacted Tableau support who have advised that this is a known issue for 10.0 http://www.tableau.com/support/known-issues (issue ID 530781) and that 10.0.1 addresses the issue.
I have since installed 10.0.1 and have no longer experienced the issue
Now it's time to move to T10 fulltime.