As the payroll is derived from the rosters, for the most part these figures would reconcile.  Format 2 of the cost analysis report was created for you guys in order to incorporate any standard allowances an employee might have that won't actually appear on a roster. So format 2 displays all costings direct from the roster + any standard allowances linked direct to an employee.  These standard allowances are apportioned across the different sites the employee worked at based on a pro rata of shifts.

Problems with reconciling different reports may occur when an employee's pay is manually edited.  For eg. A roster costs a shift to earn a particular shift\leave loading.  Person doing payroll decides to change this for whatever reason and manually edits the pay to produce a different pay figure to the one calculated by the system.  As the rosters have not been altered the cost analysis report will show costings as per the costings on the shift, whereas a payroll based report will show what was actually paid.

Due to the way the system is designed, it is always good practice that if any amendments need to be made to either payroll or invoicing, that if at all possible, the rosters are modified to reflect the required changes. Whilst the functionality to edit pays etc is available, other avenues should always be considered first.  Modifying rosters will carry changes throughout the entire system and makes reconciling and auditing a much easier process.

I hope this helps explain the contents of the 2 reports and makes it a little clearer as to where the cause of your reconciliation problems may lie.  Basically, if you can identify differences in your reports and which employees may be affected, check those employees for payroll amendments in order to pinpoint the cause of the inconsistencies.  Remember that the cost analysis report is designed to extract costing data from the rosters not the individual pays.

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