In addition to a variation while the line is accelerating/decelerating, I would expect to see a difference between the cutoff length at constant 100 FPM and constant 500 FPM.
Presumably, you are maintaining a constant air pressure to the cylinder and the distance between the blade's rest position and the edge of the web is constant. Given that, it will always take the same amount of time for the blade to reach the web and start cutting. But at different speeds, that constant time represents a different amount of paper passing by a fixed point. Your speed compensation should add or subtract from the cut setpoint. At higher line speed, you command the cylinder to extend at a slightly lower preset.
I don't know the details of the Aromat HSC, but many brands include a 'counts per time' value in the data that the HSC reports to the PLC. That would be the basis of your speed compensation. Also, if the HSC has direct-acting outputs that aren't subject to the PLC's scan time, you can use that to eliminate additional variation.