Just a thought, but, here's what I do. I use a wood conditioner on alot of fretboards, it is a paste that basically does what lemon oil does, it conditions the wood giving it a long long life, it also seals the pores a bit, and conceals any minor scratches. However, if you apply it wrong (ie, don't wipe it off in between it's cure time and hardening time) it could possibly chip I suppose, although, to miss that time, you really have to miss it, you have a good 48 hours to wipe it.
I can't imagine clear on a rosewood or ebony board. If it is ebony, I have seen highly polished ebony, and the surface of it can chip as well, and almost appear like a paint chip, this is because ebony, ironically is a fairly brittle wood, it doesn't act like any other wood, if you plane it, or sand it, it's almost liek a chalk, it doesn't cut like rosewood or maple. It's also very messy, when it gets to dry, it can flake, crack, or chip, is it possible you're looking at ebony boards that are chipping? for what it's worth, I have seen some crappy ebony that is very very light looking almost like dark rosewood, I did an inlay on a custom neck with a piece of ebony that I didn't believe was ebony until I started working with it, it was grainy, and not black like ebony normally is.