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Compare Jobs does not correctly compare layers with different names?

By default Compare Jobs (menu: Tools | Compare | Jobs...) will look for layers with the same name (between both Jobs).  However if the other job does not use the same layer name there are two additional options in dropdown Map Layers By which you should try:

Stackup order (Layer Type):

Compare layers using the same stackup order between Jobs.   For example on Job #1 a layer with type: "Top Silk"  will be compared against Job #2 a layer with type "Top Silk".

Synchronize Layers:

When selected the option will use the command "Synchronize Layers" to make sure all layer names and types map correctly between multiple jobs.  Synchronize layers is primarily used during Panelization, but is very useful for Compare Jobs, especially with the layer names between jobs are different.

For more information about Compare Jobs,

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