This problem can also occur when using the Wildhorse probe
with most breakout boards, especially those that use current
from the input pin flowing through an opto isolator.
The reason there is a problem is that the current that
lights the LED in the probe is effectively a leakage current
that must flow through the input terminal of the G540 or
breakout board. An external resistor can help divert most
of the leakage current away from the breakout board input.
In the case of a PMDX-125 or PMDX-126, an external pull-up
resistor to +5 volts can solve the problem. We recommend a
470 ohm resistor. Next time we update our design, we will
make a provision on the board to add this resistor internally.
In the case of the Geckodrive G540, the internal supply is
12 volts. There are two problems posed by the G540. First,
the resistor values needed to work with a 12 volt supply
become impractical due to excessive current through the
probe and second, the G540 does not bring its internal 12 volt
supply out to an externally available terminal.
Your solution of wiring the probe backwards so that the LED
does not conduct is probably OK, but be aware the most
LED's specify a reverse breakdown voltage lower than 12 volts.
Opening the probe and clipping the wire between the LED and
the resistor inside will eliminate the leakage current that prevents
the probe from working with a G540.