Hi Jason,
If your site has an SSL certificate and you have things configured as recommended in the article Use SSL, then if you somehow get redirected out of SSL (ie to an url using http instead of https), then your cookies will not be passed in the insecure request (to protect them form possible cookie theft), so in this case it can appear that your are logged out because on insecure requests the authentication and role cookies are not passed in the request headers. However mojoPortal is designed to try to keep you in SSL once you have established a secure connection, so if that is what is happening I'm not sure what is redirecting you out of SSL.
You may also need to check in page settings to make sure you have not enabled browser caching of the page, the browser could be caching the version of the page without the toolbar when you are not authenticated.
Hope that helps,
Joe