I am not sure what is causing your issue. You might have some corruption in your database. You can try to export your drawing using the export command, saving it as a dwg and selecting all of your items and see if that fixes it. If not, you can try a trick that I do to create "Live" sections.
For every section that you need create a new blank view drawing and xref your model drawing. Draw a polyline around the area that you would like sectioned making sure that your polyline is placed in the correct locations. Then using the polyline xclip your xref to remove everything outside of the polyline. Once the xref is clipped change your view to match the sectioning line of the xref. You will now have a live section that will update automatically whenever you update your model. You can change your ucs to match your view and annotate to your hearts content.