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I haven't really dove in deeply into them but from what I understand (and I'm just a fan of weather) each computer model "sees" something different (which is a good thing so we're not blindsided by something unexpected, but that means we have lots of possibilities too). They're programmed differently. Some are biased towards something or don't handle certain situations well (say location of certain weather systems nearby), etc.
Hopefully they still agree, but when they don't they're having a hard time understanding what's around them. They also have a proven record to generally handle very weak systems poorly which accounts for a lot of the current disagreement we see on 99L. If we actually get a Tropical Storm the models will hopefully come into much more agreement.
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