MacOS – Where does Synergy store the crypto setting? I want to turn it off

You should make sure that in your /etc/apache2/users/username.conf you have the following:

<Directory "/Users/username/Sites/">
    Options Indexes MultiViews FollowSymlinks
    AllowOverride All
    Order allow,deny
    Allow from all
</Directory>

The FollowSymlinks and AllowOverride are essential here. While you are hinting at both in your question, maybe you did not configure these correctly in tandem.

Make sure in httpd.conf /private/etc/apache2/extra/httpd-userdir.conf is included as well. It is by default.

After any modifications, restart the web server for the changes to take effect.

If you are still having problems, maybe there is a problem with your actual rewrite rules. Were you using them in a .htaccess context before as well? Note that in a .htaccess, the rewrite rule regex is matched against a request URI without the leading slash and always relative to the directory where the .htaccess resides, whereas in a global httpd.conf the URI must match with a leading slash and is relative to the web root. Because assumedly you have your .htaccess in a subdirectory of ~/Sites, your rewrite rules might behave different from when the .htaccess resides in the web root of a (virtual) host.

To debug mod_rewrite you can enable rewrite logging. You should enable that in /etc/apache2/httpd.conf:

RewriteLogLevel 3
RewriteLog /path/to/rewrite.log

This happened to me while in Snow Leopard. It's a different situation, however I fixed it by removing the mail account, and re-adding it fresh. Worked forever after that.

-Z