Actually, the parameters don't show up in Joomla 3.1.5. Or at least the List ID parameter is missing for a User List menu item.
For those who may be interested, if you want to use external links with sh404SEF turned on, the only way I could get it to work was to manually create a URL in sh404SEF. The SEF URL and the non-SEF URL had to be identical, which is the complex URL that CB supplies when going through the Joomla core. Then assign that same URL to an external link.
A large downside is that the dropdown list at the top of each list is ignored ... changing the selection will always return the first list in the database.
In my case, Joomla SEF did work with all the lists as long as sh404SEF was turned off. But even in that case, you need to create menu items as external links to the proper list with the Joomla-supplied URLs.
With either Joomla SEF or sh404SEF, you can find the URLs by using the dropdown list at the top of a given list so long as sh404SEF is turned off. Change the list and copy the URL that results. The menu item created with that link will work with both Joomla SEF and sh404SEF (with the caveat that you have to create that URL manually in sh404SEF). You can also create more pleasing aliases in sh404SEF for that URL, although they are of minimal benefit.
I realize this isn't optimal and doesn't work for diogotu, but it will work for me until CB 2.0 comes out. I hadn't seen this written down explicitly anywhere in the forum, so I thought I'd add this post in case it helps anyone else.