The boycott was a major international setback for a quick reoccupation of NEI needed to end the Japanese occupation of the archipelago. The Brits had taken-over Allied control in SE Asia from the Americans and had been put in charge of the liberation of NEI. They in turn wanted to handover control to the Dutch as soon as possible and like the Dutch Government they put pressure on the Australian Government to break the boycott.
Lord Mountbatten the newly appointed South East Asian Allied Commander (SEAC) did want to see the Dutch getting back to NEI as soon as possible. He flew into Sydney to try and persuade the trade unions to stop the boycott, all to no avail. It was not until March 1946 that the Dutch were finally able to take over control of the NEI.
This needs to put against the background of the great overall international shortage of ships. The Dutch ships caught in the boycott were desperately needed in the global post-war effort. However, the Australian Chifley Government was unable/unwilling to break the ban. The union movement in Australia was simply too strong. Controversially there were several actions from the Australian Government in this crisis that can only be interpreted as tacit support for the Indonesian cause.