When a filter is applied in a report in Reports & Analytics, the total for the line items still shows the overall total or the site wide total. When specific dimension values (specific line items) are added from the Analysis Workspace search bar to the report, the report gives two options to calculated the sum. These two options are:
1) Calculate totals by summing the values currently in each column.(gives the sum of the selected line items only)
2) Calculate totals based on all rows for each metric. (gives Site Wide total)
If the totals are different in Analysis Workspace report and the Omniture report, make sure that the first option is not selected. The setting needs to be enabled by clicking on the gear button in the dimension name's tab:
Now, select the second option under "Column Totals" so that the totals match in both the reporting platforms.