Thanks for the bug report! This behaviour looks like it was caused by a recent change in WP Super Cache’s functionality that caused it to cache the unmodified version of the page, rather than the modified version.
I’ve just pushed a new version of HTML Cleanup (v1.2.4) which should fix the issue – I checked with WP Super Cache’s default settings on a test website and it worked for me. (It may take a few minutes for the updated version to appear in your plugin list. Alternatively, you can uninstall / reinstall HTML Cleanup to get the latest version immediately.)
Please let me know if this fixes your problem!
David