Advancing Runners

Was just going over my loss in my league's World Series last year and noticed that I lost the deciding game on a DOUBLE**/SINGLE** split with bases loaded, where all runners scored!!??!!
Never mind that the 5-6 roll was the only sure hit on Seth Lugo's card--stuff happens. But the fact that it explicitly states that runners advance two bases, yet the winning run scored from first, makes no sense. Anyone understand how that happened???

The game uses super-advanced running rules and some maximum rules, at least one of which doesn't always follow the */** symbols.