If you have, for example, a 10-page document and only some of the pages are converting, there are a few reasons why this may be occurring.
You are running an evaluation version. The evlauation version is limited to converting up to 3 pages at a time. You can convert as many times as you like, but never more than 3 pages at once. If you are using the Enterprise batch conversion feature, the application will convert 3 pages of each document.
You created a layout for only some of the pages. If you have the "Pages Different" option selected, you will need to create a layout for each page individually. Go here to learn more about marking tables/fields and go here to learn more about creating layouts.
You've set the page range so that only some pages will be converted. If you want to convert all the pages, make sure the range is properly set to include all the pages. Learn more about Page Ranges under the Job Summary section on this page.