This post was taken from http://www.dieseltruckresource.com/dev/showthread.php?s=&threadid=38829&perpage=15&pagenumber=4
The hesitation will be fixed by the re-flash. It has to do with the ECM being temporarily "confused" by the missing tooth in the tone wheel. When it happens, the pilot injection is partially lost and sometimes if you get it just right the pilot injection is not given at all and that cylinder misfires. Its a very small "area" of the torque curve, so it shouldn't happen at WOT or light throttle.
The hesitation will be fixed by the re-flash. It has to do with the ECM being temporarily "confused" by the missing tooth in the tone wheel. When it happens, the pilot injection is partially lost and sometimes if you get it just right the pilot injection is not given at all and that cylinder misfires. Its a very small "area" of the torque curve, so it shouldn't happen at WOT or light throttle.