Make sure you get an encoder that has high resolution. My customers have used several brands that seem to work just find. Danaher, BEI, Stegmann come to mind.
Now think about this. If the encoder that in monitoring the line speed is subject to that much shock, what do you think that is doing to the encoder readings. The output of the encoder must be accurate and smooth since it is what the rest of the system is geared to. The motion controller should have some way of monitoring and graphing the lines speed and the speed should not have noise on it.
Another issue is that the shear does not match the line speed. This can cause the encoder to stall or pull which then affects the shear speed. The problem amplifies itself.
The same effect can be seen to a lesser degree caused by the shear pushing the metal down while shearing. When the metal is pushed down it pulls on the up and down stream material. This in turn affects the encoder rotation and the speed of the shear.
The point is that you must make sure the mechanical part are right.