Ok, so you need to make sure which is 'flash' and which is 'running'. You can also check both connections by applying 12VDC and seeing if they come individually.
It all depends on how it is wired inside. If the same LEDs are used for both functions, running and flash (dual intensity), then you will need to make sure about your wiring assuring that you have running connected to the aux connector and flash connected to the old signal wire. Make sure the flash is grounded. If there are separate diodes for each, then I suppose it really shouldn't matter.
I am not exactly familiar with those lenses, so my answer is purely speculation.
Try this. Plug the 'running' that you got to work to the blinker, see if it blinks. Try the other connector to the running, see if it lights when activated. This should at least tell you if you're unit is working properly.
I assume you have the same problem on both sides of the bike?