Could you email me a full test document that I can use to reproduce this issue? Please send it to support at htmlvalidator dot com.
I would also like to know whether you are referring to JavaScript Lint messages, HTML Tidy messages (which should not check JavaScript), and/or CSE HTML Validator's own messages. I know that CSE HTML Validator will stop checking after a specified number of errors or warnings, but that setting should not have an effect on the other checkers (they may have their own limits though).
I did a little investigating with the file that you sent.
The problem appears to be that JavaScript Lint is not checking the scripts at the bottom of the document in the sample/test document that you sent me via email.
This appears to be an issue with JavaScript Lint. It may be "getting confused" by some of the earlier syntax.
May I send the document you supplied to the developer of JavaScript Lint? Thank you.
jsl doesn't understand <%= and <?php, so it's failing with a syntax error. Since jsl stops on the first syntax error it finds in a file, further errors are not reported.
He indicated that he is working on a new version which also fixes this issue where a syntax error stops the checking of the entire HTML file. I hope to incorporate this update into a future version of CSS HTML Validator, but will want to make sure it's considered a "stable" version first.
I suspected it was failing after errors, since some pages had the issue and some didn't. Since I moved most of my inline scripts to the bottom of the page to improve performance, I no longer have the script checking due to several <% %> tags in the body of every dynamic page.
Thanks for the update. Looking forward to the updated version.