Strange story.
In last few years I've driven,along with masses of Italian reg cars across the It-Sl border near Trieste, Goriza and Treviso. Didn't see a single official. In one city -Goriza - the streets cross backwards and forwards between the two states.
Must have been an unusual spot check and the insurance aspect sounds the most likely.
In any event Italian car-hire companies usually make no problem ,or small charge, for allowing their cars into Slovenia. They usually stamp something - I never checked what -on the car-hire papers when you tell them you intend driving across a border.