After days of trying all kinds of things I got the triggers working again. I even talked to cInput support and here's what they said:
"0. It may be resolved with something as simple as rebooting your system.
1. If you have multiple controllers plugged into your machine, try unplugging all but one. It may be necessary to reboot for this to have any effect.
2. If you have multiple controllers, try plugging in at least two of them. Again, you may need to reboot before Unity will recognize this change properly.
3. Sometimes the triggers will map differently, sometimes both combined on Axis 3, and other times separately on Axes 9 & 10. If you're trying to read input from the triggers on Axis 9 or 10, try it out with Axis 3 or vice versa depending on your circumstances.
Note that the Keys class included with cInput will try to detect the Xbox controller and map the triggers to Axes 9 & 10 but due to these intermittent issues it doesn't always work. So you may not be able to rely on the Keys class in your efforts to get the triggers working properly.
I know this is a hassle and I'm sorry. Unfortunately, due to the fact that cInput is merely a wrapper around Unity's input manager, and because the bug exists in Unity itself, there isn't much more that we know of that we are able to do to fix this issue once and for all."
In case anyone has similar issues here's what I did for the UFE input options using cInput:
Imported cInput
Made a new input in the UFE Global settings.
Input Type: Button
UFE Button Reference: Button 7
cInput Button Name: P1LeftTrigger
cInput Default Key: Joy1 Axis 3-
cInput Alternative Key: none
Button Icon: Button 7