No problem, Michael.
In the version of the Ledger / Financial Reporter you have, it is possible to create the desired account-department combinations using the RNGMERGE function. The Help file has good detail on how to use this. The easiest way to see this in action is to create a new statement using the drag-and-drop method from View / Account Groups and select the Departmental Comparative option and your two departments.
In the next upgrades to Adagio Ledger and FX, this will be much easier to accomplish. The concept of 'Department Lists' are introduced, where a set of non-consecutive departments can be selected to include in a group that may be selected from the department drop-down, just like for ranges or masks.
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Regards,
Softrak Tech Support