I am currently developing a new Drupal-powered site and experiencing problems with the default HTML filter. I can change the settings all I want, and they always save themselves properly. But they seem to have no effect on the text being displayed in the posts or comments.
Regardless of whether I tell it to strip tags or comment them out, it will comment some out (usually real tags, like <cite>, <code>, or <a href...> which are supposed to be allowed), and others will be stripped out (usually, but not always, things that users have typed with angle brackets like from other script-like languages). It is quite random in what it chooses to be stripped or commented, but is consistent once it has made its choice. I copy the text from a post where it is stripped and paste it into a new post and it might get commented instead.
So as if that wasn't strange enough, the real kicker is that it can't possibly be a problem with the filter files or related. This is because the site experiencing the problem is one part of a Drupal 4.6 multi-site installation. The other site, obviously running off of the same code, works absolutely flawlessly.
Some things I have tried include repeatedly resetting the filter settings to default, rebooting the server, copying the filter files over again with a re-downloaded Drupal (just in case), deleting posts and reposting them, and probably a whole host of really minor desperate shot-in-the-dark type things that had no effect either.