It's definitely puzzling.
As you note, when he has a losing record over almost 350 racks played, the sample is huge and the rolls are 100% irrelevant.
Enjoyment
My best guess is that Shane doesn't enjoy the experience of being accountable to anyone else but himself. That may be why he thrives at Derby City, the US Open and, more recently, the World Pool Masters, but never looks comfortable at the World Cup of Pool or the Mosconi. This year, I think being named a captain made things even worse for him. Shane is no leader and when he's not leading by example at the table, asking him to lead the troops is a bad idea.
Modified Routine When not Playing a Match
I also wonder whether having to remain in the arena while he is not playing cramps his style. Most players have their own routines when it comes to down time and sweating matches rarely is part of those routines.
Loose Pockets and Slidy Rails
I also think the fact that the Mosconi is played on bucket tables with slidy rails has hurt Shane in three ways: 1) it reduces his breaking edge, 2) it reduces the edge he normally enjoys for being a phenomenally straight shooter and pocketer --- everyone can run out on such easy equipment, and 3) it exposes some of his limitations in kicking, for Shane has shown poor adaptability in his kicking game when he plays on very slidy tables.
Make no mistake about it, Shane is a fantastic short race player. The Derby City 9-ball was races to seven until 2012, and Shane won over a field of hundreds twice before they switched to longer races.
Needless to say, this is all speculation, but it's my sense of it.