ok basicly the way this mod works is the LED is getting 5V all the time but no ground (so it's off) when you plug a controller in it grounds the shielding on the port and turns the LED on...
the pics aren't very good in the tutorial because honestly although I wrote it I never actually did the mod
(just got a ton of requests for a tut because I figured out how to do it).
make sure when you're testing the port you're pluging in a whole controller and not just the dongle... because just the dongle will not turn on the LEDs
(probably the biggest mistake people make when doing this)... usually if it were wired wrong it would be on all time.
as for your port LEDs check to make sure they're not interfearing with anything, a lot of time dongle LEDs or port LEDs do weird things to cause this and other mods to not work right, but it seems that it's almost always a really easy fix.