Keyboard heatmap not accurate

I have a Macbook Pro running OSX 10.10.1 and I am running WhatPulse 2.5. The overall keycount seems to be accurate on the Input tab, but the heatmap is not accurate for modifier keys such as Command, Option, and Control. For example, if I type “COMMAND C”, the overall counter increments by 2 and the C counter increments by 1 but the Ctrl counter is not incremented. I have also experienced issues where pressing “SHIFT (any key)” results in the SHIFT key counter not being incremented although that bug only happens intermittently.