I made some slight changes to logtokens (little tokens used for login purposes). Now your logtoken used for login sessions (i.e, the one in your cookie, also used for SOAP) is different from the one used for Atom/RSS feeds (e.g., your main index.pl feed, which allows you to have your homepage preferences reflected in your feed).
If you have problems with cookies, logtokens, authentication, etc., let me know.
Update: I had to "invalidate" all logtokens so they could not be used for logging in. They still work for Atom/RSS. This just means you need to re-log-in the next time you go to the web (and may need to also fix your logtoken or cookie for use with SOAP etc.).