Okay, speculation... I'm guessing what the algorithm does is pick a number of lesser vaults, then populate them to dungeons in a specific order. Eg... game rolls 2d4 lesser vaults. PC:6 gets the first one. UD gets, let's say, 0-4. In 1.1.1, CoC gets the rest. In new versions, however, random dungeons also get a few. Since CoC gets whatever is left, it gets depopulated due to the random dungeons, and on low rolls often gets zero.
Likewise, I'd imagine that the game rolls 0-4 greater vaults, and assigns two to D:45/6 and IQD at the outset, so in 3 out of every 5 games you don't see more than two.