If the late payments are lowering your credit scores, they are on your credit report. MyFICO provides you with scores based on your official credit reports, not on the reports that MF shows you as a CMS. While this information is identical 99% of the time, there can be inconsistencies between what a CMS shows you and what your actual real hard-copy reports show you. If your score is being held back by late payments, they are present on your real credit reports. Your best bet would be to obtain copies of them to see for yourself what exactly is on there.
