The May Motorcyclist says:
Stop out over the wires, not in the center of the lane
If the layout is square, stop over the wires parallel to the road to use all of the bikes length to present a bigger "target" for the sensor to "see"
Round patterns are the same, but a little more difficult to get lined up efficiently over the wire
Try putting the kickstand down over the wire or running the starter motor to provide a bigger magnetic field
Go to www.greenlighttrigger.com
and get the big freakin' magnet and strap that under your bike
If all else fails, use the "The light is obviously malfunctioning" defense, be safe, and ride through.
Again, these are MC magazine's suggestions, I have not tried the kickstand or starter thing (though on my bike if I try the kickstand, I WILL be trying the starter), but next time I get stuck I will probably give it a shot.
Hope this helps!