Accessibility Checker

When I run the accessibility 'full check' I get the standard three manual remidations, Language, logical reading order and clolor contrast.  I then pass all of the suggestions and save the document. When I close then reopen the document, the color contrast and logical reading order need to be passed again, the approval is not sticking. This is resulting in the siteimprove flagging the pdf as not accessible. Is there a step or something that I am missing to get those manual remidations to stick? Thanks for the advice.