Sounds like phenol poisoning. I have had this happen several times too. protocorms look great, then over a matter of days to a week turn brown. The problem is that some seedlings exude phenol toxins, poisoning the agar and themselves. Phals are notorious for this.
Some agar seems to be more prone to this too. Westerns media seemed to do this more quickly for me than P6668 if not kept in aircond.
The only thing you can do is replate the protocorms often and more quickly. Always keep back up seed of each species incase this happens.
Brett
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