Greg,
It certainly sounds like the turbo is dumping boost. That is still a puzzler though because the larger balance tube in no way raises or lowers manifold pressure. It just equalizes existing pressures more efficiently between manifolds. Since it doesn't change manifold pressure, it shouldn't change airbox pressure and thereby shouldn't effect boost. Does the TCU measure manifold pressure or airbox pressure? If it monitors airbox pressure for regulating the boost, the TCU would not know the balance tube had been changed.
The mystery deepens.
Bill.