When you used the Input Map application, did each individual LED light up correctly for both controllers? There's also a test app (SimpleLEDtest.exe) you can use to confirm the hardware is working correctly. When you purchased the LEDWiz controllers, did you specify different USB IDs?
If hardware is not the issue, then turn on the Debug Log and Verbose options, run some games, then email me the \ledblinky\debug.zip file so I can take a look.