Issue: Problem with new lines

Any help with this?

For example if edit the front page of the wiki and add the code:
After save it become:

If you are using PHP 5.5, then it might be a side effect of this warning, which happens when saving all posts:
vBulletin has special instructions for turning off error reporting when PHP is 5.4 or higher. You may need to do this.

You should check your error logs for any other error messages when you save posts as well.

I can confirm this behavior on this site, but I will not be able to debug it until I return from vacation, since our server no longer allows remote dev access.

Yup, unfortunately this is caused by the Warning messages generated by vBulletin's WYSIWYG parser under PHP 5.5. You can complain to them about it. I tested and once all the /e modifier messages are fixed by "using preg_replace_callback instead", the line breaks behave as expected. You can click "Preview" instead of save if you want to see the messages I mean. A more generic explanation, although I can no longer test it since we patched vBulletin here, is that:

When submitting WYSIWYG mode, line breaks become literal "r" or "n" (no backslash) if the line break occurs inside a BB-Code tag that supports WYSIWYG. You don't really need to prove the behavior, just tell them they are using the /e modifier in includes/class_bbcode.php and includes/class_wysiwygparser.php when that modifier poses security risks, is deprecated, and may no longer work properly in PHP 5.5.

It was unclear in your first post, so I prematurely closed the issue quoting a vBulletin bug. But here is some more information:

The "rn" issue in most wiki pages is due to the vBulletin bug.
However, the "rn" issue in the wiki index page is due to a caching issue. See: https://www.vaultwiki.org/issues/3634/