I am sowing orchids here in Brazil. I have tried to replate protocorms after 3 and 4 months, but somehow up to 50 % of them end up oxydizing, turning brown and dying within the first 72 hours, the surving seedlings however, live to be very strong - much stronger than those which are not replated.
What genus are you working with? If they brown in 72 hours I'd say it is definitely a problem with the replate media. As Montera suggests, It could be a pH problem but that affects nutrient availibility so I'd guess it would show effects more slowly.
My guess, the replate media is too strong and is giving the sensitive little guys fertilizer burn. Try making your replate fourmula at about 75 or 80% strength. You might have to add back a bit more agar if you want it really stiff but I use it on the soft side and it works just fine with most.