It sounds like the lens has alter the shape of the focus of the LED beam. Instead of the original footprint size of the OEM die for that Cree LED, you probably made it larger with the lens. Imagine a SST-90 with no reflector and that's probably what driver is seeing. If that is the case, then I think a deeper reflector may help here. It may help reduce the glare and retain more of the light into a forward projection.

In your original post, you quoted a "Custom made lightening system". By that, did you use a standard reflector for the that led or a small reflector that fitted the requirment for your housing? Matching a right reflector with the led you are using will change the aspect of the beam immensly, and even more so if you have modify the led with a lens as you did. If you can provide a picture of the LED in the reflector may help here. Personally I never builded my own flashlight nor bicycle lights, but I have looked into it, and from what info I gather in the past, this might just be the problem you are having.