Your injection pump has a sensor that detects if both cylinders are pumping properly.  This is detected by a sensor that is mounted in a passage way between the two cylinders.  If both pistons are pumping properly, the pressue between the cylinders should alternate causing the sensor to alternate ON and OFF.  This is the sensor with the blinking red LED.  This LED should blink during normal operation.

This sensor activates the FLOW ALARM message when it is either bad, not adjusted properly or in fact one cylinder is not pumping properly.

The actual rate of the product flow is determined by another sensor that is mounted on the pump and measures the speed of rotation.  The speed of rotation and the Cal number determine the amount of product being pumped.

Your Injection module compares the ratio of the two sensors in an effort to determine if there is a problem.  Apparently your system feels that this ratio is incorrect.

I would attempt to adjust the first mentioned sensor.  It is attached in a slot so that its relative position can be moved.  There may be other problems with the sensor since it sounds as if you are quite certain that you are applying the proper amount.