Okay, I think I've nailed the source of MY problems, I can't really comment on anyone else's. but I was using the "auto unlock" shortcut for my switch widget app. That particular function doesn't really play nice with GB at the moment.
Sometimes even when I had the lock screen disabled, it would still lock at times. I don't think GB notifies you if your screen is already active when the notification comes through, and I'm assuming (<--key word) that using a 3rd party app to disable the lockscreen whether it works or not, tricks the OS into thinking the screen is active. Once I stopped doing that, I noticed my LED worked as normal. Even when using Gmail notifier and SMS popup to take advantage of the different color LEDs
Another conflict is with SMS popup. I had this set up to turn on my screen when a SMS that I assigned a popup comes through, Whenever that happened, even if I didn't mark it as read by responding to or closing, I wouldn't get the LED. However, once I disabled the "turn screen on" feature, the light functioned as normal.
So in short, it seems that if your screen is on at the time the notification comes through, you WON'T get the LED.