I think what he was saying is that Vinnie played the backbeat slightly 'behind' the beat deliberately, a musical decision determined by the mood or feel of the song(This works really well for medium slow R&B tunes and most ballads, for instance).
I'm guessing this was unlikely software related because this was the 90's and DAWs were probably NOT as prevalent(if that's what you're referring to)...but I know what you're saying. Latency can create problems in the studio for the inexperienced engineer/producer.
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