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If a toolbox in ArcMap or ArcCatalog is created within the ArcToolbox Window, the next time the application is opened, the toolbox is not listed.
The custom toolbox was not saved.
Right-click in empty space anywhere within the toolbox and select Save Settings > To Default.
This saves the toolbox reference to the default template; the normal.mxt for ArcMap and the normal.gxt for ArcCatalog.
As an alternative, the toolbox settings, including any custom toolboxes, can be saved to a file and loaded on demand, instead of saving to the default template.