Hi Nick
first if your using the charge pump try switching it off to disable it
just incase there is a problem with the 10KHz signal being sent to printerport pin 16
it could be the switch mode power supply you have does not work with the G540 you have
in one thread here I have read have had an increasing number of G540's sent back for testing and found its the power supply at fault
or you have a version of the G540 that needs sending back to Geckodrive for modification
as they found the resistor that is used to measure the supply current needs changing - they made a production change to fix the problem
contact Geckodrive for instructions to fault find your G540 and depending on the result return for replacement
John