Peter, not being too technically minded about this, but I would suggest you will find differences with any artificial light source. Obviously nothing is quite as efficient as good old natural sunlight. When I first started building these, I considered using the old standard light bulb, but they tend to give off a rather orange glow and their life was far too short, this is why I opted for bright white LED's. The odd reading may well be a function of the diffuser material I am using as well, this is an opal shade opaque 4mm perspex.
As you say I don't believe that there is any adverse result in the function of the light box. Thus far I have built around 100 of these and as far as I can tell by the lack of negative feedback, everyone is happy with the results that they are getting.