There can be a large difference in scores for the very reasons you stated. If the negative items are recent, the more impact they have on the score and if one report shows no negatives, it would be high. Whereas the ones with the negatives would be considerably lower. Depending on your credit age, negatives are likely to have a larger impact as well. One collection dropped my score 50 points, luckily, it was an error and I was successfully able to remove it.
Just wondering, didyou pull them all from my fico? Where all accounts showing the same reporting dates for the good accounts?