Beautifier provides several options to clean up WP's messy (X)HTML source code output, such as code indentation.
This plugin provides a bunch of options to change what WordPress is sending to the browser. The text sent to the browser is called HTML/XHTML and you can usually see it by doing a right-click on the page and select something like "View Page Source" or "Show Sourcecode". This plugin provides the ability to indent all lines correctly for easier reading, the removal of unnecessary whitespace characters, the ability to remove anything you want from the output using regular expressions and a few other options.
The reason for that is most likely a invalid or missing Doctype declarations (DTD). This plugin only takes action, if a valid (X)HTML DTD is found in the first 200 characters of the page. If you don't know what a Doctype declarations is, read this article about Doctypes or see this list of valid doctypes for (X)HTML documents.
To narrow down the cause, start disabling every single option (under Settings->Beautification) one by one and see if the problem persists. If it persists, deactivate the plugin and copy-paste the working generated (X)HTML source code into a txt-file; afterwards activate the plugin again and copy-paste the broken (X)HTML output into another txt-file. Send these two files to the author with a short description of your problem.
Try the Reset Options button in the Settings menu under Beautification. If that doesn't help, deactivate the plugin and contact the author. To resolve your problem faster, attach your server's PHP error-log-file to the email.