The fact is that Marvel set what allowed the Proto-Adamantium to exist a total unknown. It is a mystery and will probably stay that way. We can only speculate on what was this unknown factor.
I believe that the unknown factor/catalyst responsible for the creation of Proto-Adamantium was the duration the mixture remained in its liquid state.
We don't know how much time was required to "heat up" each subsequent tested mixture and most importantly we don't know how long MacLain was asleep.
An alloy is successfully created once its multiple components are heated and melted together at their common melting point and have successfully bonded. The mixture is then poured into a casing and allowed to cool.
When the components are melted there is no gain at leaving the mixture in a liquid state any longer.
During his experiments, MacLain combined Vibranium with a steel alloy
he was working with. While asleep, as a result of his exhaustion, an
unknown factor caused the metals he was working with to bond. MacLain
was never able to duplicate the process due to his inability to
identify a still unknown factor that played a role in it. (Captain America Vol 1 #303)
With all the varius components only one was susceptible to cause an unknown factor in the experiment, Vibranium. It is possible that Vibranium, which is extraterrestrial in origin, didn't behave like any other metal know to man. It could have changed over time in its liquid state and begun a molecular reaction with the experimental steel alloy and others components resulting into what is known as Proto-Adamantium.
This process requiring a significant amount of time to occur, could have allowed the molecular structure of the Proto-Adamantium to stabilize as the mixture remained at its melting point longer than intended.
As a scientist, in an attempt to replicate the shield alloy MacLain must had recreated the experiment methodically and logistically without leaving the mixture in its liquid state longer than necessary. It is possible that he never thought about leaving the mixture in its liquid state for a prolonged, since for all he knew couldn't make any difference and instead logically reproduced the experiment without trying any unorthodox methods.
This scenario could be the reason behind the formation of Proto-Adamantium and why it was never duplicated.