Hi Michael,
Unfortunately, I do not think they are protocorms. They may have started that way, but what they are now is not that. Each mass on the gel medium started as a single protocorm. There were only 6-7 seeds that germinated from that batch. So each lump you are looking at is only 1 seed.
Also this flask is 9 months old. That jar was flasked in February of 07.
Instead of making leaves, the potocroms just kept producing round "ball" like cells. They got bigger and bigger, even sometimes toppled over from the weight of the piles, but never grew into anything.
For comparison’s sake, both the normal and abnormal jars are all Cattleya's species. However, the normal looking jars that are showing leaves were flasked on June 20, 07.
No other jars have ever looked liked the monster flask. So, I still don't know what is happening in that jar.