If you have a document that contains text boxes within shapes, Acrolinx might not be able to find any issues in the text boxes. This could be because you've converted documents from .doc to .docx format. During the document conversion, information about shapes gets lost and Acrolinx is not able to get the text.
Acrolinx can extract text from text boxes within shapes from .docx files when the text boxes are created in that format. You can recreate the documents in .docx format and Acrolinx will then happily check your document.