The troublesome years of Bourke, his erratic behaviour and apparent mental problems, his difficult disengagement from the Benedictines and from New Norcia, as well as his temporary exile from Western Australia, ignored by most scholars until now, are mentioned by Dr. Teresa De Castro.
[7]: 342–343 The normally mild-mannered priest caused some sensation at a public meeting prior to the election by suggesting violence would result if state aid were lifted.
[8] The battle was ultimately lost—the MPs who had supported him lost their seats at the election, and in late 1895 the Government passed a bill bringing the funding arrangement to an end.
In August 1894, he resigned as Vicar General, desiring to retire to New Norcia, but changed his mind thereafter, deciding that the number of Catholics arriving in Western Australia due to the gold rush and the cause of maintaining the private schools justified his continued presence.
He became a Monsignor in 1898 and the inaugural parish priest for West Perth in 1901, residing in the Presbytery of St Brigid's in Fitzgerald Street for the rest of his life.