That should not be the case....I have a Flextone III XL and MK2 shortboard....However, I don't think I have ever really used it with the Flexy. Always use the old MK1....I will try to check that out for your this evening...

Have you done the calibration?

source: http://line6.com/support/docs/DOC-4501

FBV Shortboard Mk. II: (Note: Before performing the calibration routine, please disconnect any expansion expression pedals IE: EX-1)

1) Hold the D button while connecting the CAT-5 cable on the FBV. The display will read “CALIBRATE PEDAL” until the D button is released, at which point it will read “1 PEDAL TOE”.

2) Press and hold the internal pedal toe-switch until the LCD changes to “2 PEDAL MIN”. This should occur instantly.

3) Set the heel to (minimum) position, press the D button. The LCD will change to “3 LCD MAX”.

4) Set the toe position (maximum) and press the D button. The LCD will change to “CHECK VALUE 127”.

5) Move the pedal and verify that the value reaches 0 in the minimum position and 127 in the maximum position.

6) Press D to exit