My 4 yo son had this happen a few times. After a visit to the Ped, Derm, Allergist and blood tests, we've discovered it was contact dermatitis. We STILL have not figured out what it is either...it's so frustrating. I think it might be from picking dandelions (sp?). I feared Kawasaki (rare-but not impossible to contract), hand/foot/mouth disease, fever can cause it/but no fever, eczema, fungus/same as athletes foot (creams didn't work), the list goes on. Before his fingers peel, they get very red and burn, so we've been able to take preventative measures (washing thoroughly and applying auquaphor or neosporin w/pain reliever).
Good luck!