How is it possible to not have many negative items on your credit report, but have low scores?

Has 4 positive items, 1 paid and closed loan, one old closed credit card and 2 open credit cards with small limits but only at P and I know it should be lower. The bureaus report them as positives.
Then there were 2 negative which came from identiy theft. And higher credit card for almost $ 1400 and some sort of public utility company for almost $ 3000. The fraud was reported and the police reports were sent in last week and overnighted for Tuesday and Wednesday. How is it that the scroes are still low if they are removing the negatives? We are trying to get a mortgage but our scores are extremly low. But even if things were not taken of I do not understand why the scores are low. We have had companies tell us (ex: a car dealership) that the credit isn’t really bad, it is just the scores are low. Any reasons why or suggestions would help and be greatly appreciated.
Opps, I thought I mentioned that I did send the reports to the 3 bureaus. That is who I overnighted the reports to.

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