We have noticed some funny things are happening to some of our PDF's after you run them though acrobat Pro to make them accessible, and then post them back to our site. It looks like they are getting changed but the modification dates are not changing. Things like commas getting moved, or misspelling, and black blocks showing up over words. The images below show how a PDF looks after it is made accessible and saved back to the web, and how the pdf looked originally.
Please let me know what version of Acrobat you are using and on what OS.
Try updating as well as repairing Acrobat from the Help menu and check.
You might refer the below mentioned KB doc links to ensure that PDF file is accessible:
Let me know if that helps.