I believe this was always the rule and was always implemented. 

It's a rare occasion a perfect score, and ever rarer that we have multiple perfect scores.

In the 6 seasons I ran the Prediction League we had (at a quick glance)

Season 52 - 2 perfect scores, Celtic on both occasions. They were wildly good at predicting that season. To the extent it started to look suspicious!

Season 53 - 2 perfect scores - Stranraer got one and then in round 7 we seen Hearts, Annan & Motherwell and get perfect scores.

Season 54 - None

Season 55 - In Round 9 Hamilton, Hearts & East Stirling claim 100k each. Then we had another Round 8 mad one. 9 Teams got a perfect score.

Season 56 - None

Season 57 - St. Mirren in Round 4 and Elgin in Round 5.

To the best of my memory, when we had multiple winners, we paid out the full 100k, happening 3 times in 6 seasons