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The Multi-perspective process explorer plug-in

Hi, I am using the above plug-in for conformance checking in ProM 6.8 which has worked perfectly to calculate the fitness and show deviations.
When I select 'Show Performance Mode' and the 'frequency' measure the total number of cases on the model is the same as in my event log. However, the case and event frequencies shown on the model and when you select an event are different to the numbers in my event log. 
I have looked for a paper on the plug-in to explain how it calculates these numbers but cannot find one.
I would greatly appreciate any advice.
Thank you, Sam
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