Like many others, we've been having a nightmare since 3.96/7 with Ubuntu 12.4 on AWS.
When updating to 3.96, most of our sites 30+ CMS sites (WP/Drupal/Magento) & phpMyAdmin had problems.
We solved most of these problems by rolling back via a server backup, and selecting to not fix the domains at update.
We've now had to (for different reasons) move our domains onto a fresh install of 3.97 and create the virtual servers via a virtualmin backup. Upon re-creating them, the WordPress sites work but the majority of our sites on Drupal don't. The only way to prevent a 500 error is to comment out 'Options +FollowSymLinks' in the standard Drupal .htaccess file. Even then we seem to have problems with the sites such as 500 errors on stylesheets, etc.
If you create a new virtual server on fresh install of 3.97 and install Drupal, it doesn't work by default. You have to edit the .htaccess file to access the site, then if you turn on caching the site's JS and CSS fails with 500 errors. This is a pretty big problem...
Can anyone help and explain how to change the settings for a new virtual server creation in 3.97, that will undo what has been added by these updates please? We can't be fixing this on a per-domain basis and I'm sure we're not the only people having this problem.