A common problem that may occur when using the Batch Wizard to validate a website by following links is that not all pages will be checked. Below are some causes and solutions for this problem.
Make sure that the follow links option is checked in the Follow Links tab of the target's properties. See the Target Properties topic.
Links may not be followed if a validation is terminated due to too many errors or too many warnings. When a validation is terminated, CSE HTML Validator stops parsing the document and stops extracting links. To limit this situation from happening for websites containing pages with large numbers of errors and/or warnings, we recommend that an "Errors only" validation be performed first. You can select "Errors only" in the 'Tool to Use' page of the Batch Wizard Options.
You may also want to try increasing the maximum number of errors by going to the 'Message Output' page of the Validator Engine Options. A value of 50 or 100 may work better. Once enough errors are corrected in the web pages so that the validations do not terminate, then an "errors and warnings" only validation or "normal" validation can be performed to find further issues.
Another solution to the above problem would be to address/fix the errors and warnings of the pages that the Batch Wizard was able to check, then process the target list again. Continue fixing the errors and warnings and then re-processing the target list (revalidating) until you are satisfied with the results. The key is to get the number of errors and warnings down so that the validations aren't terminated (due to too many errors or too many warnings) and all the links can be extracted, followed, and validated.
Another possible cause of pages not being checked are mismatched quotation marks. An extra or missing quotation mark in or around attribute values may confuse the parser. If this happens, then the document cannot be parsed properly and links may not be extracted. If this is the case, then many of these messages will be generated: "This line contains part of a quoted string that spans more than one line (not recommended) or a quoted string (like an attribute value) that is missing the start or end quotation mark. Check this line for improperly quoted attribute values that may be missing a start or end quotation mark. As currently configured, HTML Validator requires that all quoted strings be contained on one line and have start and end quotation marks. Note that because of inconsistent handling by user agents, it is not recommended that attribute values contain line breaks.", but only if the allow multi-line quotes option is not checked in the 'Attribute Options' page of the Validator Engine Options. Look for these messages and correct the problem, then re-process (revalidate) the target list.