Verify the footswitch with an ohmmeter. You should find that each of four pins should have continuity to pin 2 of the connector when the switch associated with the pin is pressed.
Note the pin numbers on the connector seem to have a weird layout. Here is a link to your amp schematic. The Footswitch interface is shown on page 3 of 12.
http://elektrotanya.com/fender_cyber-twin_sch.pdf/download.html
Use the ohmmeter to check each wire in the cable is good. SOme cables, unless the official one for the unit, may lack some wires.
The amp "reads" the footswitch state into a register which is then read serially. The inouts are pretty well protected from user mistakes. With the schematic you should be able to analyze the failure.
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