The main cause of this issue is that the Comparison rates have been updated into the Estimate, they have then subsequently been changed in Comparisons and not updated into the Estimate to apply the changes.
To confirm this, first run off the Comparison Job Summary to Excel
Input/Output, Comparisons, Job Summary (displays what is in the Comparison)
Once exported open the Excel File and use the 2nd Tab called Trade Order
Then go to ConQuest, Analysis, Estimating, Job Resource (displays what is in the Estimate)
Compare the Job Resource figure with the Comparison Gross Total Column (Sort the Job resources list by description to match the Excel file)
Mark any differences and then go back to those trades in Comparisons and run the Update again. They should now match.