You should NOT put a jumper cable across pin 1 and pin 5. That would be like putting a 0-ohm current set resistor across those terminals.
From the Gecko instructions:
Wire your motors to the included DB9 solder cup and secure the backshell connectors. If your motors are rated below 3.5A you must use a current set resistor across PIN 1 and PIN 5. The resistor is calculated by taking the current in amps and multiplying by 1000. If your motor is rated at 2.8A per phase you will have to use a 2.8K 5% 1/4W resistor. If your motor is rated at 3.5A or above you can safely not use a current set resistor; however, your G540 will not go into current standby mode which will result in increased motor heating.
So, you can either leave pins 1 and 5 unconnected, or if you would like your G540 to go into current standby mode when it is inactive (to reduce motor heating), then you should connect a 3.5K resistor across pins 1 and 5.
(Note: 3.5K is not a standard 5% tolerance resistor value. The nearest standard 5% resistor values to 3.5K are either 3.3K or 3.6K. I don't think that it's critical, but you could hand pick one that is closest to 3.5K, or just choose a 3.3K.)